France's Pierre Rolland (Cannondale-Drapac) finished third.
Briton Geraint Thomas, who had gained some ground back in Tuesday's time trial after his ninth-stage crash, was unable to follow the top guns in the last climb.
Dumoulin (Team Sunweb) kept his cool despite repeated attacks from Italian Vincenzo Nibali (Team Bahrain) and Frenchman Thibaut Pinot (FDJ) to stay 2:23 ahead of Colombian Nairo Quintana (Movistar).
(This story corrects final paragraph to show Nibali with Team Bahrain, not Astana)
(Writing by Julien Pretot; editing by Mark Heinrich)
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