Ex-Formula One racer Brendon Hartley won for the number eight car while Argentina's Jose Maria Lopez finished in second place for Toyota - two minutes after Hartley.
British team Jota were triumphant in the second-tier LMP2 class as another ex-F1 driver won - this time being Will Stevens while Glickenhaus finished third and fourth.
Richard Westbrook of the UK and America's Ryan Briscoe and France's Franck Maileux of the 709 Glikenhaus finished third - five laps ahead of the 708 of French duo Romain Dumas and Olivier Pla alongside Luis Felipe Derani of Brazil.
Alpine had a race to forget after technical difficulties meaning that they could only muster 23rd position overall.
In fifth was Jota's 38 car - which was driven by Mexican Roberto Gonzalez and Antonio Felix da Costa despite being fourth for a large proportion of the race.
The other Jota car, however, came in seventh following a sensational race by Oliver Rasmussen.
Swiss driver Sebastien Buemi and Japanese star Rio Hirakawa - in the number eight Toyota car - swapped positions with number seven throughout the race but the Japanese took control of the Circuit de la Sarthe event.
"I'm jealous of Brendon," said Hirakawa. "Next time, I want to do it!"
Movie driver Michael Fassbender - who drove a Porsche 911 car - ended up finishing 51st overall and 16th in the GTE AM amateur class. The Irishman, 45, had a low finish due to a few spins and a heavy crash in practise.
Next year, Le Mans will celebrate its 1000th anniversary in the sport for its hyperclass and it will be boosted by the return of a Ferrari team as well as Peugeot. It is the first time they will be competing in the race since the 1970s.