As Wout Van Aert took his first career Tour stage win, Thomas and Ineos team-mate Egan Bernal were among those to profit hugely as French rival Thibaut Pinot was caught in a group that lost 100 seconds.
The 217.5km stage from Saint-Flour had been billed as a dull transition day before Tuesday's much-needed rest, but when riders awoke to see a stiff breeze blowing, they realised it would prove anything but.
Deceuninck-Quick Step's Julian Alaphilippe finished in the front group – having done much of the work to split the peloton – to retain the yellow jersey, while Mitchelton-Scott's Adam Yates, UAE Team Emirates' Dan Martin and Movistar's Nairo Quintana were also among those to capitalise.
AG2R La Mondiale's Romain Bardet was also in the front group to claw back some of the time he lost on La Planche des Belles Filles last week, recovering to 15th overall.
The action began when Rigoberto Uran's EF Education First put the power down with 40km to go and successfully split the peloton, only to find themselves slipping into the second group on the road as Alaphilippe himself took up the baton.
Team Ineos and Bora-Hansgrohe then helped out as Pinot's Groupama-FDJ team struggled to keep up in a group which also included Astana's Jakob Fuglsang, Trek-Segafredo's Richie Porte and Uran.
"EF had a little go and then Quick-Step," Thomas said. "We're just always attentive and ready. It was a really good day in the end.
"We had everyone bar two guys and we all just really committed. Bora were there, there were plenty of guys turning. Behind, you can tell they went full on the climb to try to close it, but because they didn't there they just ran out of gas and that's when the elastic snapped.
"On a day like today you'd never expect it really. It was just a positioning error from them and they've lost over a minute and a half so it's great from our point of view."
The new-look GC sees Thomas in second, 72 seconds behind Alaphilippe and four seconds ahead of Bernal in third, with the 22-year-old Colombian taking the white jersey as the best young rider.
Yates moves up to seventh, still one minute 47 seconds down, while Martin is in ninth, a further 22 seconds back.
But Pinot will curse his luck as he dropped from third place to 11th, now two minutes 33 seconds off yellow.
Stopped by French TV cameras immediately after the stage, Pinot said: "We dealt with it like s**t!" and promptly rode off.
Van Aert edged out Alaphilippe's team-mate Elia Viviani to deliver a fourth stage win of the Tour for Jumbo-Visma, who will celebrate all the more given their general classification hope Steven Kruijswijk also got himself in the front group to sit fourth overall, 87 seconds off yellow.
"I'm sorry, I can't believe that I've won a stage of the Tour de France," said the 24-year-old Van Aert.
"It's above anything else. I've discovered this race in the last 10 days. Winning at my first attempt is incredible."