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The Lotto-Belisol rider completed the stage in 4:11.39 on Thursday, which was just ahead of Norwegian Alexander Kristoff who was classified as second.
Astana's Vincenzo Nibali, who was also part of the leading group at the end of the stage, retains the yellow jersey, while Peter Sagan, also up with the leaders, keeps the green.
"It was a nervous day and I'm happy with my team," the German winner told BBC Sport. "They kept me near the front especially with the sidewinds in the final 13km to keep me in a good place.
"I had a good wheel with Mark Renshaw but with 250m to go I said to myself I go full now and whatever happens happens. There was a lot of pressure on us but we had a good answer today."
Jakob Fuglsang is second in the overall classifications.