Geraint Thomas's second consecutive stage win was greeted by booing and whistling at the climax of an ill-tempered stage during which Chris Froome was shoved by one spectator and the former Tour de France victor Vincenzo Nibali was brought down by a race motorbike.
Fellow Brit Chris Froome also managed a podium finish in a stage that took the riders 108.5km through the Alps from Albertville to La Rosière, crossing the line third to move up to second overall - almost 90 seconds behind Thomas.
Thomas continues to say he's riding in support of Froome - who could tie the record of five Tour titles - rather than to win cycling's biggest event himself. The action from Bourg-Saint-Maurice to Alpe d'Huez will be broadcast live on NBC Sports Network.
"Team Sky tried to keep both riders in GC", Dumoulin said as he warmed down on the rollers after the stage.
Thomas extended his lead over Froome in the overall standings to 1 minute, 39 seconds.
Greg Van Avermaet, the Rio Olympic road race champion, went into Wednesday with the yellow jersey and a 2:22 lead, which he had tripled on the first mountain day Tuesday. Thomas did make it to the powerhouse and while the Welshman trounced away solo to the stage victory and the yellow jersey, Dumoulin limited his losses, finishing just 20 seconds behind the new yellow jersey. He finished in a group 22 minutes after Thomas.
Van Avermaet is a super one-day racer but not a strong climber.
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The Italian rider was able to remount his bike and by the summit only lost 13 seconds to stage victor Geraint Thomas (Team Sky) but was in clear discomfort.
"I'm speechless", said Thomas.
And having won the opening stage past year to wear yellow for the first time, Welshman Thomas revealed an extra determination to don the famous colour for another day.
The 12st stage of the Tour de France is always one of the most special and Geraint Thomas's historic victory made Thursday's ride one to remember, however there were also a couple of unsavoury incidents. "You expect professional athletes to play and entertain without being impacted on by the crowd".
"Whatever happens now is bonus", Thomas said. Froome has six Grand Tour titles, including the past two in the Giro and the Vuelta a Espana. He knows how to race over three weeks. I knew that I had something left.
However, Nibali got up and managed to finish 13 seconds adrift of stage victor and Team Sky rider Geraint Thomas.