Froomey still has our best chance now - there's still more than half the race to go.
'I had a little gap and then obviously Froomey could follow the guys then.
"It is unreal - I didn't expect it", he said.
Yet Thomas, a former track cycling Olympic champion like 2012 Tour victor Bradley Wiggins, has yet to prove he can handle the pressure of a grand tour.
The 115-km final stage of the race is on Sunday, July 29 and goes from Houilles to Paris Champs-Elysees.
The differences between the main challengers were essentially made in the team time trial in the second stage.
The selection, as is often the case on the Tour's first mountain stage, came at the rear of the group, where Rigoberto Uran (EF Education First-Drapac) and Ilnur Zakarin (Katusha-Alpecin) were among those distanced.
Froome, who is eighth over all after nine stages, is 1 minute 42 seconds behind yellow-jersey holder Greg van Avermaet before the first Alpine stage on Tuesday.
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. 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. I think it's fantastic for us to have those options. Jakob Fuglsang of Astana was next at 3:12.
The 109 km stage from Albertville to La Rosière Espace San Bernardo was the second stage of the tour to take place in the Alps, following yesterday's finish in Le Grand Bornard. He wore the yellow jersey for four days a year ago - before dropping to second behind Froome - then crashed out on a descent in Stage 9. While Valverde quickly dropped back, Dumoulin kept up his pace and was only surpassed by Thomas.
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. 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.
Sprinting standout Mark Cavendish, meanwhile, finished far behind and missed the time limit, ending his Tour.