By catching Dumoulin, Thomas had already done enough for yellow but wanted more as Nieve slid into view, kicking again to pass Nieve inside the final 400 metres and take the stage win.
Julian Alaphilippe soloed to victory on stage ten of the 2018 Tour de France as the race entered the Alps for the first time, while Greg van Avermaet produced a superb ride to extend his overall lead.
Asked whether his performance, and his claiming of the yellow jersey, had changed anything with respect to leadership duties at Team Sky, Thomas was unequivocal.
Froome is 3:21 behind Van Avermaet after recovering from a punctured tire atop the second of the stage's ascents, finishing with Thomas and most of the top contenders.
Indeed Team Sky were so unconcerned that they allowed Van Avermaet into the day's breakaway, probably expecting him to blow up somewhere on the four mountains on the 158.5km from Annecy to Le Grand-Bornand.
Though the sight of Sky massed on the front of the peloton most of the day was not one to excite fans, Thomas delivered the stage win with panache.
But Van Avermaet, who predicted he would lose the yellow jersey before stages Tuesday and Wednesday, cracked on the second of three major climbs Wednesday.
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Dumoulin then attacked on the descent of the penultimate climb, the Cormet de Roseland, linking up with Valverde before the road rose up again towards La Rosiere. Froome initially held back, marking counter-moves from AG2R La Mondiale's Romain Bardet and UAE Team Emirates' Dan Martin before leaving them both behind.
"Obviously, Froomey is the leader", Thomas said. That gave him extra time to soak up the applause from the French fans for the country's first victor in this race, two days after France won the World Cup.
The prospect of having "six riders riding in the mountains from the start with other teams attacking, it's going to be a lot more hard than with the eight riders".
"I feel some guys might sit here and give some PR bullshit but I just say how it is with me and that's how it is".
Froome punctured a tire 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.
"I knew there was a good chance". "To do it two years in a row is really nice".