Fueled by previous disappointments and thoughts of his ill father watching on TV, Alaphilippe timed his break perfectly and powered to victory on the first day in the mountains, crossing the line alone, and finishing well ahead of his rivals for his first Tour win.
Team Sky's Chris Froome has finished the 12th stage of the Tour de France in the fourth position and maintains the second place in the General Classification.
Julian Alaphilippe claimed France's first victory on this year's Tour de France when he climbed impressively to win the 10th stage on Tuesday, a 158.5-kilometre ride from Annecy to Le Grand Bornand.
That saw the Belgian extend his overall lead to two minutes and 22 seconds over Thomas, with Movistar's Alejandro Valverde up to third, three minutes and 10 seconds back.
Dumoulin, the 2017 Giro champion, refused to see the day as a lost opportunity to shake Team Sky, the dominant force in the peloton. "Seeing them in October, we talked about it and said we would just have to try", Cavendish said after the stage. "He did it the last time he had the jersey".
"I am speechless", said Thomas.
On Monday's rest day, 2012 Tour victor Sir Bradley Wiggins had suggested his old team would "have a real problem on their hands" if Thomas took yellow ahead of Froome - who is 59 seconds back on his team-mate in sixth place.More news: Secret recording of Trump-Cohen on payments to adult-film actress emerges
Cycling - Tour de France - The 156.5-km Stage 9 from Arras Citadelle to Roubaix - July 15, 2018 - BORA-Hansgrohe rider Rafal Majka of Poland and Team Sky rider Chris Froome of Britain in action. Over the years, we've always tried to build teams where the top guys are very close together and they have got their own ambitions.
"We were pretty happy to have the numbers up front".
Froome was momentarily slowed down by mechanical mishaps on a gravel path atop the second climb up the beyond-category Montee du Plateau des Glieres, the first use of a dirt road by the Tour since 1987.
"It little bit wacky races going on there", the four-time Tour victor said. "It was a little bit of a comedy of errors going on there".
On the four Tours Froome has won, he has worn the yellow jersey after the first mountain stage.
There will be two more stages in the Alps with a summit finish at the iconic Alpe d'Huez, but fireworks should not be expected as the top guns are likely to hold fire, waiting for the finale in the Pyrenees. "It's a long way to Paris but I'm really happy to have this one for a minimum of one day". "I can have a super good day after a rest day and go over the limits but I pay it back..."