Their manager described it as nothing more than anecdotal but it was historic too. This was an achievement, even for the club that reached a Champions League semi-final despite being from a town so small that every person resident there could go to the Camp Nou and they’d still leave 50,000 empty seats. The club that left behind a quarter of a century in tercera, Spain’s “third” division which is really anything from its seventh to its 24th, to play 16 seasons in primera and 12 in Europe, boasted a European Golden Boot and made three European champions and a World Cup winner. They’d been to the San Siro and Old Trafford but they’d never been here before: Villarreal are top of the league for the first time ever.

Villarreal have been Copa del Rey semi-finalists, European Cup semi-finalists, Europa League semi-finalists and La Liga runners-up. In 2006, Juan Román Riquelme missed that penalty and they missed out on the European Cup final. Every time they had the chance to go top, even if it was only for a moment, something seemed to make them stay, as if, when it came to it, one of the advantages they enjoyed became a disadvantage instead, as if the lack of pressure became a problem. Seven times it happened and twice they had the chance to go top alone at the end of the jornada, in 2007 and again in 2010, only to draw with Almería and Hércules. Not this time.

On Saturday, Real Madrid could not score against Málaga and Celta drew 1-1 in Eibar. The opportunity was there but Villarreal’s opponents were a different prospect this time: Atlético Madrid, the team who had sent them down in 2012, league champions two years ago and the team who had taken striker Luciano Vietto off them, their top scorer last season. In return, Villarreal had signed Léo Baptistão on loan, scorer of just seven league goals at Rayo Vallecano last season and only one at Real Betis the year before. Atlético had not applied one of those cowardly crapping-yourself clauses, perhaps because they weren’t crapping themselves. Perhaps they should have; Baptistão scored the game’s only goal.

And so it was that 576 top-flight games later Villarreal became league leaders, for the first time in their 92-year history. Look at the table and it reads: Villarreal 16, Barcelona 15, Real Madrid and Celta de Vigo 14. “I don’t feel anything,” said Marcelino García Toral. “It’s a passing sensation, nothing more.” Villarreal’s coach, sometimes over-excited schoolboy, other times a stern school master, seems to enjoy being contrary. And, anyway, his words were belied by the celebrations down in the dressing room where players embraced, bounding around a table piled with food, shouting, clapping and cheering, before slumping elated but exhausted on to the benches by their lockers.

On one level at least, Marcelino is right of course; this is anecdotal. Villarreal are the 40th team to have been sole leaders of the league and only nine of them have ever won it: Barcelona, Athletic Bilbao, Madrid, Atlético, Betis, Valencia, Sevilla, Real Sociedad and Deportivo de La Coruña. Of the teams currently in the first division, only Málaga have never been top and everyone bar Granada has been there for more weeks than Villarreal. They will not stay there either, and not just because other teams are stronger, but because they will not maintain this run. Yes, they have won five from six, and beaten Atlético too, but the other sides they have faced are Betis, Espanyol, Granada, Athletic and Málaga: 10th, 9th, 20th, 17th and 18th.

Yet this is not chance and nor is it unimportant or without merit. Instead, it serves to underline their achievement. Marcelino took over Villarreal halfway through the 2012-13 season when they were down in the second division and although things did not look good, he brought them up, then finished an extremely impressive sixth place. Last season, they finished in the same position, while also reaching the semi-final of the Copa del Rey and the last 16 of the Europa League, where they were defeated by the eventual winners Sevilla. At one point they went 28 consecutive games scoring and a Champions League place seemed possible.

It’s true that they slipped away, as Marcelino said they would, unable to compete consistently in Europe and the Cup; true too that by the end, some players were exhausted and some even wondered if their manager’s obsession with weight, reinforced with daily tests and the strictest of limits imposed, might have been counterproductive. They won just two of their last 14 games and there may be a warning there. But the very fact that they had got themselves into that position in the first place was impressive as it was telling.

And yet this start still surprises – if not so much that Villarreal have got it right, then that they have got it right so quickly. In the summer, 10 players left and 11 players arrived. They lost their entire forward line: Vietto went to Atlético, Gerard Moreno Balagueró joined Espanyol and Ikechukwu Uche is now at Tigres: their three top scorers had gone. Joel Campbell, a winter signing, went too. And Giovani dos Santos went to Los Angeles Galaxy. They’d already sold Gabriel halfway through the season.

Even if some at the club think with hindsight that relegation was useful institutionally, forcing them to confront their debt and restructure, and even if they were among the bigger clubs in the second division, their annual playing budget has fallen. It stands at €61.5m, the sixth biggest in primera but some way behind the top five: Sevilla €105.1m, Valencia €122.8m, Atlético €156.9m, Barcelona €421.7, Real Madrid €431.3m.

Sales remain inevitable but rebuilding is one of the things that they do well and this summer Villarreal handled it intelligently; their forward line is probably better now, not worse. They raised €37m (plus the money for Gabriel, which could rise as high as €19m) and spent €43m bringing players in. The two Samus, García and Castillejo, had joined from Málaga before the market had even got going for a combined fee of €16m; they brought in Adrián and Baptistão cost-free and signed Cédric Bakambu and Roberto Soldado.

Soldado is perhaps the perfect example of how it fits together. Now playing in a team whose style suits him, working in an environment that has aided him, a kind of perfect ecosystem, he has scored twice and provided three assists, the latest to Baptistão on Saturday night. No one in La Liga has more. Bakambu has scored three times. It is working.

This weekend, Villarreal equalled the start they had under Manuel Pellegrini in his best season at the club and many have said that, under Marcelino, his style has been recovered. They’re wrong: this is a much more dynamic team, more vertical. Marcelino wants players who are comfortable on the ball and insists that “compatibility” is more important that talent alone, but he is more interested in dynamism, in pace and precision on counterattacks, prepared to wait if needs be, to sit deep ready to release players quickly. It is great to watch and successful too. And here they are. In two and half years, Marcelino has taken Villarreal from the second division to the top of the first.

“Anecdótico” he called it, and it sort of is, just not entirely. It mattered. The club’s president, Fernando Roig, insisted that the reason he was pleased because they had picked up 16 points, meaning that they were closer to the 40 they would need for survival. More pertinently, if they are to fight for a European place, and maybe even a Champions League spot, they already have a significant advantage over those with whom they compete: they’re 13 points ahead of Athletic, 11 ahead of Sevilla, seven in front of Valencia and four ahead of Atlético.

In the long term, that will matter. But as players gathered in the dressing room and fans reached for the paper, grinning like Zippy as they tore out the table, what mattered more was that right now Villarreal are at least one point ahead of everyone else in Spain for the first time ever.

Talking points

• When the ball dropped, he was ready for it. A neat flick, first time with the outside of his foot, sent it to his right-back, dashing up the line. Suddenly, Real Sociedad were away, running at the Athletic Bilbao defence. A couple of quick passes opened space, the noise rose, supporters began to stand and then … nothing. The shot was blocked, the move ended, and that was pretty much that. The man who started the move, the man who produced that one moment of skill amidst the madness, adjusted his suit. And then David Moyes sat back down again. The Basque derby’s best touch and it came from the manager.

David Moyes during the Basque derby. Photograph: Jose Ignacio Unanue/NurPhoto/Corbis

The Basque derby is special, or at least it’s supposed to be. Of the 22 starters, 17 were Basque and Sunday began with the Bertso Derbi; two teams of Basque street poets taking each other on, verse versus verse, on stage at the Teatro Principal. In the old town there were flags and flares, in red and white, and blue and white too, while la Real’s fans marched together to welcome the team bus. But it was hard to avoid the sensation that something was missing: fans, for a start. Fewer Athletic supporters had made it than usual, the usual mix reduced, and there were 6,000 empty seats. Above all, there wasn’t much football. Those who missed it missed little.

Outside the ground you could buy an egg for a euro and throw it at your choice of four students, two in Athletic shirts, two in Real shirts, should you wish. No one took a shot there and there weren’t many shots inside either. There wasn’t much football, full stop. The ball went long to one end and then came back again, usually taking the same route. By half-time, during which la Real’s sporting director Loren Juarros García huddled out the way by the presidential box, puffing on a cigarette, there had not been a chance. By the end, there had not been many. Sure there were moments when Bruma and Williams came on but they were fleeting ones.

At full-time, there had not been a single save, only one genuinely good chance wasted – for Sergio Canales – and perhaps one decisive moment, when Asier Illarramendi slid in and blocked a shot with his arm: “I would have protested too if it had been the other way round,” he admitted. But that was about it; no goals and not much else either. “I didn’t have any work to do,” says the Real Sociedad goalkeeper Gerardo Rulli, saying it all. Athletic’s Gorka Iraizoz could say the same.

The front page of El Diario Vasco described it as “turgid”; Marca called it “nothing”; and El Mundo went for “insufferable”. That was perhaps a bit harsh, and four points from the last six eased the tension a little on Moyes, but this game was not great. And if the Real Sociedad manager intended it to be a compliment when he called it “quite British”, not everyone took it that way. His touch had been the game’s best. Touch was not really the word for what everyone else did: mostly, the ball flew from one end to the other, over people’s heads, both managers offering the same explanation: it’s true that there was too much long ball, they said, but sometimes when the pressure is on and the intensity high, there’s no other way. And so it got booted about. Up in the main stand, commentating for Canal Plus, the former Liverpool striker Michael Robinson remarked: “They’ll be carrying the ball off on a stretcher soon.”

• Speaking of the hand ball, Ernesto Valverde was asked if he has any idea what a hand ball is these days. After all, last year every time the ball hit an arm, the free-kick/penalty was given and a card too, while this year referees seem to have noticed the word “intentional” in the rules and they’re not giving anything. “They tell us at the start of the season: in fact, we pretty much end up doing a Masters on it,” Valverde said, laughing “… and then each individual referee has his own interpretation anyway.”

• Real Madrid drew, Atlético Madrid lost, but Barcelona lost most of all. Leo Messi controlled a long pass, a superb touch taking him into the area, but as he went to shoot, he was blocked, his knee twisting. As he went down, the Camp Nou fell silent. He tried to carry on but could not. The game went on without him, Luis Suárez scoring twice in a 2-1 win, but people were more interested in what was happening at the hospital up the road. In the end, it was confirmed that he had torn the ligament in his knee and will be out for around six to eight weeks, maybe returning just in time for the clásico in November. El Mundo Deportivo’s front page headline summed it up: “Gulp!”

• Madrid took 31 shots, Cristiano Ronaldo 14 of them (this column made it 13, actually, but anyway), but they could not find a way past Málaga. Rafa Benítez put it down to bad luck and a little “anxiety” in the final minutes but the truth is that there was also something a little unconvincing about the way Madrid attacked at times, lacking a little subtlety (lacking James Rodríguez most of all?). Carlos Kameni was in save-everything mode … until one slipped through his fingers and on to the line. Over the line perhaps? It would be easy enough to put goalline technology in. But, hey, then all those TV shows and media mass debates might (or let’s face it, might not) have to find something worthwhile to talk about instead of just shouting at each other from familiar trenches. And we can’t have that.

Carlos Kameni keeps the ball out against Real Madrid. Photograph: Angel Martinez/Real Madrid via Getty Images

• Kameni stopped everything this weekend, but Antonio Adán stopped even more. No one made more saves than the Betis keeper. He was superb against Sporting in Gijón in a game where there were three goals, all of which were brilliant. One of them was Joaquín’s first since returning to Betis.

• Lucas Pérez: brilliant. He scored twice in a 3-0 victory over Espanyol and has got four goals already this season, He’s leading a side who, under Víctor, are far better to watch than they have been in recent years. Far better, full stop. They’re sixth and they deserve to be.

• Yevhen Konoplyanka scored a belting free-kick in the 86th minute to rescue Sevilla, getting them their first league win of the season and taking them off the bottom of the table and up to 16th. Two-nil up, Sevilla had seen Rayo deservedly take it back to 2-2 before he got the goal. Next up for Sevilla: Barcelona.

Results: Valencia 1-0 Granada, Barcelona 2-1 Las Palmas, Real Madrid 0-0 Málaga, Sevilla 3-2 Rayo, Villarreal 1-0 Atlético, Eibar 1-1 Celta, Sporting 1-2 Betis, Deportivo 3-0 Espanyol, Getafe 3-0 Levante, Real Sociedad 0-0 Athletic Bilbao.