That victor was Groupama-FDJ's Thibaut Pinot, who finished six seconds ahead of Alaphilippe, who in turn extended his overall race lead over Thomas by 36 seconds to now lead the race by 2:02.
"Not the best day", he said. It was okay, just that last bit I didn't really feel like I did it. "I was quite weak".
As Alaphilippe made the 18 percent slope ahead of the home straight the noise was deafening as victory over time-trial specialist Thomas unexpectedly materialised.
He said: "I just gave everything, especially the first part, I went full gas". I didn't really attempt to follow when they kicked.More news: JCPenney To Hire Restructuring Firm: Can The Retailer Avoid Bankruptcy?
"It's disappointing. I just tried to limit the damage".
At the end of the 14th stage, however, it was Alaphilippe who extended his overall lead over the defending champion to more than two minutes to give the host nation real hopes of producing its first race victor since Bernard Hinault in 1985.
Thomas's Ineos co-captain Egan Bernal finished 1min 36sec off the pace to drop down the rankings and lose his white jersey to Alaphilippe's teammate Enric Mas, who is now fourth.
Ineos came to the race with two hot favorites in Thomas and Bernal.More news: ESPN reasserts political talk policy after attack on Trump
"I was overheating a bit, It was that last bit that got me, in the last 8km I didn't have the power I wanted", he admitted.
"One more day in yellow, I couldn't ask for anything better". From the start I just didn't feel great today.
"I'm happy to profit from this exceptional moment I'm having", Alaphilippe, 33rd a year ago, was quoted as saying by the Tour's website. "It is still going to be interesting because a lot of riders lost time".
At the bus a few kilometers down from the pass, head sports director Nicolas Portal explained that the team must talk and understand what they will do in the coming seven days.More news: Emery confident Arsenal will soon have 'three or four' new players
A hundred years on Alaphilippe is tantalising France with belief growing they can win a first Tour since 1985, when Bernard Hinault clinched his fifth Tour and who was on hand to congratulate the victor on the podium. "The Tour is still long, so we'll see".