The Mitchelton-Scott rider powered away in the final ascent, a 16.3-km stretch at an average gradient of 6.2 percent, and dropped all his rivals to beat Belgian Dylan Theuns and Spain's Jon Izagirre by eight seconds.
Overall, the 25-year-old now leads Izagirre by 11 seconds and the Spaniard's Bahrain-Merida team mate and brother Gorka by 12 seconds.
Overnight leader Luis Leon Sanchez of Spain (Astana) cracked with six kilometres left and slid down the rankings.
"In the final climb, Astana controlled the pace but (team mate) Roman (Kreuziger) and I decided to accelerate and we went for it," said Yates.
Sunday's final stage is a tough mountainous 110-km ride around Nice.
(Reporting by Julien Pretot; Editing by Pritha Sarkar)
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