The Frenchman crossed the line ahead of Katusha-Alpecin's Ilnur Zakarin and Bahrain-Merida's Vincenzo Nibali at the end of the race's final day in the mountains, with pink jersey Nairo Quintana (Movistar) finishing on the same time.
The climbing specialists did what they could on the challenging parcours to put time into Sunweb's Tom Dumoulin, who is likely to outdo them in Sunday's time trial finale, but the Dutchman delivered a strong ride to limit his losses on the general classification to just 15 seconds.
Quintana remains atop the overall leaderboard with Nibali now sitting second and Pinot in third, but Dumoulin, 53 seconds down, looks to be in a very strong position ahead of the race against the clock in Milan.
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