Thibaut Pinot exploded the status quo in the Tour de France, blowing both Geraint Thomas and Julian Alaphilippe off his back wheel in the Pyrenean mist, as Simon Yates took his second stage win at the summit finish to stage 15 at Foix Prat d’Albis.

Pinot’s attack, six kilometres from the rain-drenched finish line, immediately put Thomas into trouble, with only his Ineos team mate Egan Bernal and the race leader Alaphilippe able to follow. But Pinot’s further accelerations distanced both riders and cut into his time deficit in the overall standings to both Thomas and his fellow Frenchman.

“It was impossible to follow Pinot, but I gave my all,” Alaphilippe said, slumped at the table during his post-race press conference. “I’m pleased to keep the jersey but I’m a realist. I know that the Alps will be really tough.”

Tour de France 2019: Simon Yates wins stage 15 as Alaphilippe loses time – live! Read more

The suspicion that Alaphilippe might struggle on the second Pyrenean stage’s steep roads, just 24 hours after Pinot’s irresistible win on the Col de Tourmalet, proved well founded, as a succession of narrow climbs eroded his energies. But after a stage that only further complicated the scenarios for the Tour’s final outcome, it was hard to tell who would be most satisfied.

Pinot, second on the stage, would be just 10 seconds behind Alaphilippe had he not lost time in crosswinds while Alaphilippe, in what may yet prove the hardest mountain stage of the 2019 Tour, hung on and still leads by 1min 35sec.

Thomas, after his initial wobble at Pinot’s attack, recovered well to limit his losses to Pinot and to claw back time on a faltering Alaphilippe, but Bernal’s superiority on the final climb may be a sign of things to come.

“I felt better than yesterday but I needed to try to pace it when it all kicked off,” Thomas said. “I got stuck behind Alaphilippe. We had to let him ride a bit and then I jumped.

“It’s a difficult one, tactics wise. I had the legs to go but I wasn’t going to chase down Bernal with Alaphilippe on my wheel. I had to wait a few kilometres and that gave Pinot time but at least the legs are responding really well.

“Pinot is going really well, but there are so many guys that are still so strong,” he added.

Yates’s attack came just under nine kilometres from the finish and took him clear of final breakaway companion Simon Geschke, of Germany. But he was pursued all the way up the final climb, first by the Spaniard Mikel Landa, who was then joined by Pinot.

“I’m very proud,” Yates said. “It is a bit different to my first stage win, because we raced from the beginning. But my objectives haven’t changed. I came here first to support my brother and secondly to win stages.”

Thomas may yet pay for the intensive training and dieting that characterised his buildup to his title defence. The defending champion’s well-documented lack of racing days and his need to lose weight quickly, the change of sponsor, the departure of Rod Ellingworth and the absence of Chris Froome as team talisman may all have derailed the efficiency of Dave Brailsford’s clinically run machine.

For all his easygoing demeanour – when George Bennett admonished French fans for booing the Welshman as he rode alongside the New Zealander near the summit of the Tourmalet on Saturday, Thomas tweeted “I think they were booing you mate” – he still does not appear to have the legs to win this Tour de France.

“He’s done a lot of work,” Brailsford said of Thomas at the first rest day, when final victory had seemed inevitable. “He’s come a long way since January.” But after an autumn spent at book launches, awards ceremonies and on Graham Norton’s sofa, it may prove to be too little, too late.

With the Alps looming, Ineos must surely move from plan G to plan B, in the wiry figure of Bernal.

“I don’t really mind who wins the race,” Brailsford said. “As a Grand Tour contender, Egan’s recovery and his ability to maintain his performance is one of his greatest strengths. The harder the race gets, the better he gets.”

Tactically, Thomas admitted he was stuck between a “rock and a hard place”, while Bernal remained diplomatic. “Geraint and I have good communication between us, and we are both honest,” the Colombian said. “We need to win the race as Ineos, not as Geraint or Egan. So we need to be honest.”