And then there was one. High up on the Col du Portet, a mountain whose beauty is matched only by its malevolence, Chris Froome uttered five words into his radio: “I am not feeling super.” Moments later the debate over who would be Team Sky’s leader at the crunch part of this year’s Tour de France, a subplot often laced with intrigue and deep uncertainty, came to a sudden end.

Froome, the four-times winner, began to drift backwards. And Geraint Thomas, freed of any obligations to his friend, knew what he had to do. First he pushed onwards past Froome. Then he brushed off the Dutchman Tom Dumoulin. And suddenly he was at the summit with an even bigger time gap over his rivals – and recognising that a first Tour victory was within his grasp.

“I think we’re in a great position,” Thomas said. “It’s unfortunate Froomey lost time but he’s still up there on the podium. We just have to keep doing what we’re doing.”

The history books will note it was the Colombian Nairo Quintana who overcame tyre and mechanical problems to win the shortest and spikiest stage of this year’s Tour – a 65km rollercoaster ride from Bagnères‑de-Luchon to Saint-Lary-Soulan. Yet this was the day many expected Thomas’s chances too to puncture. Instead it was Froome who fell away, losing 48sec to his teammate in a dramatic finale, with the Irishman Dan Martin finishing second and Thomas third – thus earning himself a 4sec time bonus.

It means that the 32-year-old Welshman now leads the race by 1min 59sec from Dumoulin, with Froome 2min 31sec back. As Froome admitted afterwards: “He’s got a pretty comfortable buffer. We just need to look after him for these next few days.”

To make matters worse for Froome, he was grabbed by an aggressive spectator during the stage and then accidentally knocked down by a policeman who mistook him for a spectator as he rode back to the Team Sky bus. One small mercy: at least the gendarme was not carrying pepper spray.

The stage, the shortest on the Tour for 30 years, began with an F1‑style start with Thomas at the tip of an arrowhead, marginally ahead of Froome and Dumoulin. But he never looked like relinquishing pole position.

Quick Guide Wiggle High5 to fold Show British-registered women's cycling team Wiggle High5 will not return in 2019, owner Rochelle Gilmore has announced. The team, which launched in 2013 and employs 17 riders plus 14 full-time members of staff, had reportedly been struggling to find a title sponsor for next season. "Thank you to all the athletes, staff, partners and especially the fans that got behind the team when we registered back in 2013 and all the way through those six years," Gilmore said. "It's been fantastic and we couldn't have done it without each other." Closure of the team leaves British sisters Lucy and Grace Garner to find a new home, while Scotland's Olympic track champion Katie Archibald also rides for the team when competing on the road. Two of the team's biggest names, Elisa Longo Borghini and Audrey Cordon-Ragot, have been linked with a move to join Lizzie Deignan in the newly-formed Trek squad. Photograph: Justin Setterfield/Velo

Beforehand everyone had expected Team Sky to ride the stage like a team time trial. Instead the first hour was more akin to a phoney war, as the grand tour contenders warily watched each other. But as the peloton chugged up the Col de Val Louron-Azet, the second of three climbs on the day, AG2R’s Pierre Latour, in the white jersey for best young rider, moved to the front and began pushing the pace for his teammate Romain Bardet.

It was an act of heroic selflessness, the 13th-placed rider overall jeopardising his own chances in the hope of getting Bardet into yellow. It barely ruffled Team Sky, who still had six riders together. Froome and Thomas even had enough energy to chat away happily.

There was still one more climb to come – and what a climb: the 16km‑long 2,215m-high Col du Portet. At 10am, more than five hours before the race began, it was already swarming with cheering spectators, union flags mixing with tricolours and Spanish and Colombian flags. Now they wanted blood.

They got it, too: 1.5km into the climb Martin attacked with Quintana chasing his tail. Then Primož Roglič, who was fourth in the general classification, had a pop. This time Froome immediately responded, while Thomas steadily bided his time and used Dumoulin and Bardet to bridge the gap.

However, Quintana and the Polish rider Rafal Majka were long gone and soon they were powering past Astana’s Tanel Kangert, who had led from the start. It was now a two-bike race but the Colombian always looked the stronger and, when he made his move, 6km out, it proved decisive.

Thomas, though, finished like a bullet train – although there were no regrets when he was asked whether he should have attacked earlier. “I didn’t want to risk anything, which was why I left it as late as possible,” he said. “Especially at altitude, as soon as you kick and go deep for five seconds it can bite you in the arse.”

Certainly it was hard to disagree with the assessment of the Team Sky principal, Dave Brailsford. “People were questioning whether he could handle those steeper average climbs than the Alps and he’s come through the test with flying colours,” he said. “He rode another perfect race.”

More controversially Brailsford then insisted it would be unwise to write Froome off, despite his struggles, saying: “His powers of recovery are fantastic.” That is certainly true. After all, he was able to recover from an even graver position to win the Giro D’Italia in May. This time all Team Sky’s efforts will be directed at Thomas.

At least the stage on Thursday from Trie-Sur-Baise to Pau will offer respite after two tough days in the Pyrenees before the riders head to Lourdes to tackle the Tourmalet.

This year the 70th miracle in the French town was officially recognised by the Catholic church. After what happened on the Col du Portet, those looking to catch Thomas had better start praying for a 71st.