Almost out of fuel, Denmark's Nicklas Nielsen took the chequered flag at the wheel of a number 50 Ferrari 499P hypercar shared with Italian Antonio Fuoco and Spaniard Miguel Molina over 311 laps of the Sarthe circuit.
The number seven Toyota GR010 hybrid of Argentine Jose Maria Lopez, Japan's Kamui Kobayashi and Dutch driver Nyck de Vries finished 14.221 seconds behind.
Ferrari's winning crew from last year -- Italians Alessandro Pier Guidi, Antonio Giovinazzi and Britain's James Calado -- finished third in the 51 car.
Last year's win was the Italian marque's first overall victory at the French circuit in 58 years.