A sense of history enveloped Molineux on Thursday night as Wolves returned to European football for the first time since 1980 but their immediate future in the Europa League looked vulnerable until Ruben Vinagre scored with the penultimate kick of the game to add to Diogo Jota’s first-half goal.

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Crusaders, who finished fourth in the Irish Premiership last season, performed stoutly and with good organisation throughout as Wolves were made to work for their victory five days after beating Manchester City on penalties to win the Premier League Asia Trophy in China.

The effects of the hottest July day on record might have played into Wolves’ hands more, as the Irish Cup winners had to chase the ball, but the Premier League side looked set to visit Belfast next Thursday with only a single-goal lead until Sean O’Neill’s blunder right at the end handed Vinagre his goal.

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João Moutinho swung in the umpteenth Wolves cross into a packed penalty area as the game ticked into its 93rd minute only for O’Neill to fumble the ball and allow Vinagre to tap home into an empty net.

In October 1980, the floodlights had briefly gone out as Mel Eves scored but Wolves could not overturn PSV Eindhoven’s 3-1 first-leg lead. The torch burns most vividly for this proud old club since they won the League Cup and finished sixth back then, and now they should have enough class and professionalism to win through to a third qualifying round against either Armenia’s Pyunik or Jablonec, from the Czech Republic, with the former winning their home leg 2-1 last night.

After finishing seventh in the Premier League and reaching Wembley for an FA Cup semi-final in which they led Watford 2-0 with 11 minutes remaining, Wolves’ first team looks capable of competing against the elite of the English game again. Whether they will have the requisite strength in depth by the time they open their domestic campaign against Leicester on 11 August remains to be seen, though Nuno Espírito Santo is confident.

Facebook Twitter Pinterest Wolverhampton Wanderers fans lap up the pre-match atmosphere in the safe standing area. Photograph: Nick Potts/PA

The central defender Jesús Vallejo was reportedly at Molineux on Thursday before signing on a season’s loan from Real Madrid while the striker Patrick Cutrone is believed to be close to signing for £18m from Milan.

There was certainly sufficient optimism around the West Midlands to attract 29,708 people to Molineux for this apparently imbalanced tie. “What’s really special is to be back at Molineux, and to be back in Europe after nearly 40 years is even more special,” Nuno said.

“[The second goal] make a difference, no doubt about it, for the second leg. But we have to look at what moment we are in, what we need to do, the things we need to improve: we need to be faster, more accurate and more sharp.”

Wolves beamed highlights of their historic 1950s triumphs over the likes of Spartak Moscow and Honved on the big screens beforehand, the friendlies which led to Billy Wright and co being labelled world champions and sparked the inception of the European Cup.

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Wolves led by only Jota’s goal at half-time, the Portugal forward striking a clean half-volley from Adama Traoré’s right-wing centre eight minutes before the interval. With 80% possession and 30 shots at goal, Wolves should have made the game safe much earlier.

Credit should go to Crusaders as they defended valiantly throughout, often getting 11 men behind the ball as Rúben Neves kept prompting Wolves attacks. Traoré, playing at right wing-back with Matt Doherty injured, was a constant source of pace, trickery and delivery as Wolves looked to capitalise on the heat.

The temperature had dropped to a balmy 28C by the second half but Crusaders were still made to sweat as Wolves played keep-ball in the final third. Morgan Gibbs-White, playing up front as Raúl Jiménez had only returned from his break after international duty on Monday, could have put the tie to bed on his own. He dragged one shot wide, when sent in by Leo Dendoncker, blasted a fine rising effort just over and then headed just wide around the hour mark. But Vinagre’s fortuitous goal late on gave Wolves a buffer that should suffice.

Stephen Baxter has led the club, for whom he played, to this stage of this competition five times in 10 years, losing 7-1 on aggregate to Fulham in 2011. “That was the best performance we’ve given – and I’ve played for six years and managed for 14 years,” the Crusaders manager said. “It fills me with a lot of pride.”

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Rangers hope a 2-0 lead will be enough to exorcise the Europa League ghosts of 2017 after missing the chance to kill off old foes Progrès Niederkorn at the first attempt. The part-timers from Luxembourg dished out one of the biggest upsets in Rangers’ history when they knocked Pedro Caixinha’s side out of the competition two years ago.

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Yet a missed a second-half penalty from James Tavernier was among a host of spurned opportunities that ensure the Light Blues still have work to do next Thursday.

Connah’s Quay manager, Andy Morrison, felt the referee “bottled it” in the key moment of his side’s Europa League second qualifying first-leg defeat to Partizan Belgrade.

With the score goalless heading into first-half added time, Serbia goalkeeper Vladimir Stojkovic appeared to take a swing at Nomads’ captain George Horan as they challenged for a cross.

Morrison felt it should have been a red card and a penalty but they received neither from Slovakian official Michal Ocenas and went on to lose 1-0 to Aleksandar Scekic’s volley, leaving the Welsh Premier League side with a tough task in Belgrade next week.

“I thought the referee had an incredibly poor night,” Morrison said after the game at Rhyl’s Belle Vue ground.