On a day of surprises, meanwhile, defending champion Geraint Thomas lost contact in the final kilometre of the brutal ascent to the cloud-clad Pyrenean pass ending 2,115m above sea level.
Surging from the mist, Pinot jumped away from a small group 200m from the line to beat yellow jersey holder Alaphilippe and third-placed Steven Kruijswijk of the Netherlands by six seconds.
Thomas, whose Ineos team has been used to smashing their rivals in the first high mountain stage of the Tour, crossed the line in eighth place, 36 seconds off the pace, throwing the British outfit’s challenge into doubt.
“It was a tough day out there. There’s still a lot more to come and hopefully I’ll feel better tomorrow,” said Thomas.
In all of their six Tour wins, the team led by Dave Brailsford had always claimed a stage win before stage 14. Thomas and his teammate Egan Bernal, who finished eight seconds off the pace in fifth place, were expected to stamp their authority on the race on Saturday.
Ineos instead remain winless on the Tour this year but Thomas refused to get frustrated.
“At the end I just knew I had to try to pace it. I didn’t really attempt to follow when they kicked,” he explained.
It was all about restricting the damage at the end of a punishing ride from Tarbes, where Pinot’s Groupama-FDJ and Kruijswijk’s Lotto Jumbo-Visma showed their strength.
“I thought it was better just to try to ride my own pace and limit my losses that way, rather than stay with them and blow up on the steepest bit at the end,” said Thomas, who now trails Alaphilippe by 2:02 minutes.
“Maybe I should have tried to stay with them – it’s just one of those days. I was hoping I’d come round a bit. On the last climb it was just a matter of staying there for as long as possible.”
Thomas also needs to be wary of the threat posed by Kruijswijk, who is third overall 12 seconds behind the Briton, and fifth and sixth-placed Emanuel Buchmann of Germany and Pinot, who are now 1:10 adrift of the Welshman.
Thomas, who had appeared to take the upper hand on Bernal after the Colombian had a disappointing time trial on Friday, now only leads the Colombian by 58 seconds and he was left hoping for better days as the peloton faces a huge test of strength in Sunday’s 15th stage.
“It was a tough day out there. There’s still a lot more to come and hopefully I’ll feel better tomorrow,” he said.
“What happened today is a big surprise for many. It was the first day of the pure battle for the overall with big climbs. Personally I felt well and that makes me happy,” said Bernal, who was told not to wait for Thomas when his team mate struggled.
“As a team, Geraint Thomas has lost some time and that’s not good. I was available to help him but, through the radio, they told me not to wait for him.
“We all have a bad day at the Tour de France, yesterday was mine. I don’t know if we can win the Tour de France. I know that the defending champion is my teammate. I won’t go against the instructions of my team. If I’m asked to help, I will do. If I’m given freedom, I’ll try to make the best of it.” The in-form man of the first week, Pinot had lost one minute and 40 seconds when caught at the wrong end of a bunch split on the eve of the rest day on Monday and he had promised he would use his “rage” to bounce back.
The 29-year-old duly delivered, looking strong during the whole ascent to the Col du Tourmalet, a 19km climb at an average gradient of 7.4%, and accelerated just before the final bend.
“Justice is done with that win today,” said Groupama-FDJ manager Marc Madiot.
“I really wanted to win that stage, I had marked it down. There were delirious scenes of fans cheering us on, I had goose bumps and I needed the taste of victory,” Pinot, who has stage wins in all three grands tours and finished the Tour third overall in 2014, told reporters.
Pinot is now sixth overall, 3:12 behind Alaphilippe, who extended his lead over second-placed Thomas to 2:02 after hanging onto the favourites’ group. “I defended the jersey like crazy today. There are some uncertainties in the race as some big leaders cracked,” said Alaphilippe, who has never previously raced for the general classification on a grand tour.
Kruijswijk is third overall, 2:14 off the pace, with Bernal 3:00 behind Alaphilippe, whose staying power was firmly under the spotlight on Saturday.
While he impressed, several top guns failed that same test spectacularly, with Briton Adam Yates finishing 6:42 off the pace and Colombian Nairo Quintana, a two-time Tour runner-up, ending up 3:24 behind Pinot.
Today’s 15th stage is a 185km punishing ride from Limoux, ending with a gruelling ascent up to Prat d’Albis.
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