The Gianfranco Rosi-directed movie had not been among the favorites for the prestigious award, handed out Saturday.
It was the first Italian film to win it in 15 years, The Hollywood Reporter said.
Other winners at this year's festival included Alexandros Avranas of Greece, who was awarded the Silver Lion for Best Director for his "Miss Violence," the entertainment industry newspaper said.
A new jury prize was given to "Jiao You" ("Stray Dogs") from former Golden Lion-winner Tsai Ming-liang.
The festival's Best Actor award went to Themis Panon, for his work in "Miss Violence." The Best Actress honor went to Elena Cotta for her role in "Via Castellana Bandiera."