Vincenzo Nibali, several minutes back, reined in his top challengers and appeared set to retain the yellow jersey after Stage 16.
But the contest for the podium spots below him was shaking up: Thibault Pinot of France appeared set to rise in the standings, while Tejay van Garderen of the U.S. was losing crucial minutes.
Rogers took a bow as he crossed the line after the 147-mile leg from Carcassonne to Bagneres-de-Luchon featuring an ascent up the super-tough Port de Bales.
Rogers, a former world champion, collected his first Tour stage victory.
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