Producers Bill Pohlad and Dede Gardner picked up the award after Malick was a no show.
The film, which also stars Jessica Chastain and Kari Matchett, received a widely mixed reaction at the festival, even to the point of drawing boos at its premiere.
But the picture currently holds a 90 percent rating based on 31 reviews on Rotten Tomatoes, a Web site that tracks reviews.
Cannes Film Festival Winners
Palme d’Or: The Tree Of Life (Director: Terrence Malick)
Grand Prix : Kid With A Bike (Director: Dardenne brothers), Once Upon A Time In Anatolia (Nuri Bilge Ceylan)
Best Actor: Jean Dujardin (The Artist)
Best Actress: Kirsten Dunst (Melancholia)
Mise en Scene (Best Director): Nicolas Winding Refn (Drive)
Prix du Scenario (Screenplay): Joseph Cedar, Footnote (Israel)
Prix Du Jury: Poliss (Director: Maiwenn)
Palme d’Or Court Metrage: Cross Country (Director: Maryna Vroda)
Camera d’Or (Best First Film): Las Acasias (Director: Pablo Giorgelli)
“The Tree of Life” is nonetheless a singular work, an impressionistic metaphysical inquiry into mankind’s place in the grand scheme of things that releases waves of insights amidst its narrative imprecisions,” writes Todd McCarthy in the Hollywood Reporter.
Fox Searchlight opens the film in the U.S. on May 27.
In other awards, Kirsten Dunst won best actress for her role in “Melancholia,” another science fiction drama written and directed by Lars von Trier, who was bounced from the festival for expressing admiration for Adolph Hitler.
The 55-year-old also won the Palme d’Or in 2000 for “Dancer in the Dark.”
Jean Dujardin won the best actor award for “The Artist” and Nicolas Winding Refn won the Mise en Scene, or Best Director, award for “Drive.”