Mara won plaudits for her part in 1950s lesbian love story "Carol", although many critics had focused on Blanchett who plays her older lover.
But the jury, led by American sibling directors Joel and Ethan Coen, decided the prize should go to the less showy performance delivered by Mara, a rising Hollywood star who leapt to fame with her performance in the title role in 2011's "The Girl With the Dragon Tattoo".
The award capped a great fortnight in Cannes for Bercot, who also directed the opening film "Standing Tall", becoming only the second woman ever to open the world's premier movie fest.
"I feel joy sharing this with another actress because it's a bit too big for me to carry alone," said Bercot in her acceptance speech.
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She thanked her director for choosing "an unknown at 46".
Mara's award was picked up by "Carol" director Todd Haynes, who said: "I'm a very lucky director... To have been able to work with actresses of the level of Cate Blanchett and Rooney Mara."
Trade magazine Variety agreed last week that Mara stole "Carol" from her better-known co-star.
"Blanchett does another supernatural act of transformation, but Mara, in some ways, makes an even stronger impression," the magazine wrote.
"Mara gives her (character) a graceful self-possession, a quiet confidence, that holds the film's focus."
She has not been short of work since, turning in a disturbing portrait of a drug-addled housewife in "Side Effects", a supporting role in Spike Jonze's "Her" and is taking on the role of "Tiger Lily" in next year's big-budget remake of the Peter Pan story.