Thomas seemed overwhelmed by his second ski station stage win in 48 hours.
Despite a distinct lack of support from the French locals, Team Sky's Geraint Thomas remains in possession of the yellow jersey at this year's Tour de France.
However, Nibali got up and managed to finish 13 seconds adrift of stage victor and Team Sky rider Geraint Thomas. He is now 20 minutes behind Thomas.
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. Only marginally behind him, the team's most high-profile rider Chris Froome appears to be taking the brunt of crowd aggravation however.
Asked how long he might keep yellow with his team-mate sat next in line and relatively flatter stages to come for the rest of the week, Thomas said: "Maybe the next few days, but this race is so hard".
The only other man to have won a summit finish up here while leading the Tour de France is Lance Armstrong. "I am just going to try to enjoy tomorrow". "I'm just going to enjoy it now". Even as I crossed the line I said: "'Is someone still away?'"
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He kept the tape on the entire round, although it did not appear to affect his play. Phil Mickelson opened with a 73, while Tiger Woods had an afternoon tee time.
"He should have been fighting for victory, " Thomas said of Nibali. "But we have to bear in mind that if it impacts on the race, as it did with Nibali today, then that's too much".
Thomas broke from his Team Sky teammates with 5.5 km to go, with teammate and 2017 Tour de France victor Chris Froome following in pursuit.
Sky's rivals were intent on redressing the balance on the third and final day in the Alps.
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Afetr Kruijswijk was overtaken in the closing kilometres, Thomas and Froome countered attempts by Dumoulin and Bardet to shake them off.
He says he's just trying to make the best of his form for now, without knowing what the full three weeks will hold for him.