"It's unreal", Thomas said.
Julian Alaphilippe, a French rider for Quick-Step, won the 158.5-kilometer (98.5-mile) ride from Lake Annecy that included four major climbs before a descent to Le Grand-Bornand in 4 1/2 hours.
"We were pretty happy to have the numbers up front".
The end result, however, was the same as most recent Tours - domination from Team Sky.
Alejandro Valverde of Movistar moved into third overall at 3:10 off the pace.
The 30-time stage victor was dropped early on and spent the entire stage off the back, but rejected a ride in the broom wagon before crossing the line 65 minutes after Thomas. I think it's great for us to have those options to be able to play when it comes down to it, especially looking at rivals that have two or three options within their teams.
Sky have talked up the benefits of having Thomas second overall, 43 seconds behind leader Greg Van Avermaet (BMC) and 59 ahead of Froome after nine stages. "I'm going to try to chill out and enjoy it", said Thomas.
Twice podium finisher Romain Bardet, hoping to become the first Frenchman to win the Tour since Bernard Hinault in 1985, has suffered from bad luck with four ill-timed punctures, including three in Sunday's stage to Roubaix.
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Team Sky riders Chris Froome and Geraint Thomas remained in the peleton for the duration of the stage and are now over two minutes behind Van Avermaet in General Classification. Look for yellow jersey hunters to pull no punches on Alpe d'Huez, as the strongest stamp their foot down and take charge of the 2018 Tour de France.
"Both riders were spat at, Froome was shoved, shorts were dropped in their direction", reports Jeremy Whittle in The Guardian, "yet it was Vincenzo Nibali who ended up prone on the tarmac, after tangling with spectators, as the leaders were blinded by smoke from flares".
The last and most feared of the three stages in the Alps this year, the 175.5-kilometre leg began in Bourg-Saint-Maurice and took the peloton over three gruelling, beyond-category climbs. "My back hurts. I had trouble breathing and now I don't feel well standing", said the Italian.
Record-chasing Mark Cavendish and Germany's Marcel Kittel are out of the Tour de France.
Geraint Thomas led out the sprint and won atop Alpe d'Huez.
Van Avermaet escaped in an early breakaway and held on when he was left all alone to struggle up the final of four Alpine passes. Froome was the only one of the Sky duo to put in a sustained attack, one that was ultimately reeled in by Dumoulin.
"It's unreal I didn't expect it at all", Thomas said.
"Maybe if I'm still right there after Alpe d'Huez (on Thursday), it's a bit different then".
Cavendish was in trouble long before the explosive end to this short mountainous stage, which was created to promote attacks.