Froome crossed third, just behind Dumoulin, who moved up to third overall, 1:44 behind.
The major question now may concern the dynamics between Thomas and Froome within Sky. Thomas has been one of Froome's most loyal lieutenants for years and Sky labeled him a co-leader with Froome entering this year's Tour.
"Obviously, Froomey is the leader," Thomas said. "He has won six Grand Tours. For me it's an unknown. Froomey knows how to win a three-week race. For me, whatever happens now it is a super successful Tour. Froomey still has our best chance now — there's still more than half the race to go.
"It is an ideal scenario at the moment," Thomas added.
Froome is attempting to match the record of five Tour victories shared by Jacques Anquetil, Eddy Merckx, Bernard Hinault and Miguel Indurain.
So will Thomas, wearing the yellow jersey, sacrifice himself for Froome on Thursday's climb up legendary Alpe d'Huez?
"It depends on the situation and what is going on in the race. If I have to pull towards the end, then I will," Thomas said. "We will see."
The top five in the overall classification is rounded out by 2014 champion Vincenzo Nibali in fourth, 2:14 behind Thomas, and Primoz Roglic in fifth, 2:23 back.
Dumoulin, the time trial world champion, is Sky's closest challenger.
"He's someone who can time-trial at the end of the Tour, too. We're going to have to keep a close eye on him," Froome said, looking ahead to the race's only individual time trial in the penultimate stage.
Greg Van Avermaet, who had worn the yellow jersey since his BMC squad won the team time trial in Stage 3, lost contact midway through the stage and finished far behind.
Sky calmly rode at its own pace and slowly caught a series of breakaway riders before Thomas kicked into action with 6 kilometers remaining.
"We were expecting attacks," Thomas said. "When they go, it is never nice to see them all riding away but we had confidence in each other and we rode really well."
Thomas, who is from Wales, required slightly less than 3 1/2 hours to complete the 108.5-kilometer (67-mile) route from 1992 Winter Olympics host city Albertville to La Rosiere Espace San Bernardo ski station.
It was his second career stage win at the Tour, having claimed the individual time trial that opened last year's race. He wore the yellow jersey for four days last year — before dropping to second behind Froome — then crashed out on a descent in Stage 9.
"To wear the yellow jersey is always a massive honor," Thomas said. "To do it two years in a row is really nice."
After going up the beyond-category ascents to Montee de Bisanne and Col du Pre, plus the second-category Cormet de Roselend, the stage concluded with the unprecedented and lengthy 17.6-kilometer climb to La Rosiere — a ski resort linked to La Thuile in the Italian region of Valle d'Aosta.
With views of Mont Blanc atop Montee de Bisanne, there was also a technical and tricky descent from Cormet de Roselend.
The first overall contender to attack was Alejandro Valverde up the Col du Pre. Dumoulin then escaped from the peloton with a downhill attack from Cormet de Roselend and joined up with Valverde on the final climb. While Valverde quickly dropped back, Dumoulin kept up his pace and was only surpassed by Thomas.
Sprinting standout Mark Cavendish, meanwhile, finished far behind and missed the time limit, ending his Tour.
