The number two Audi R18 E-tron Quattro of Marcel Fässler, André Lotterer and Benoit Tréluyer finished first in the endurance race, ahead of the number one sister car of Lucas di Grassi, Marc Gené and Tom Kristensen.
For most of the race Toyota's TS040 Hybrid appeared to have the advantage over Audi and Porsche on raw pace, but the number eight car was caught up in a dramatic multi-car accident during a heavy rain storm on Saturday afternoon.
The same incident accounted for the number three Audi of Felipe Albuquerque, Marco Bonanomi and Oliver Jarvis after it was struck from behind by a GT car at high-speed.
Unlike the Audi, the Japanese machine was able to continue after repairs in the pits, and Anthony Davidson, Nicolas Lapierre and Sébastien Buemi recovered to claim third place by the end.
The number seven Toyota, which had qualified on pole position, led for most of the night in the hands of Alexander Wurz, Stéphane Sarrazin and Kazuki Nakajima, but it fell victim to an electrical malady in the early hours of Sunday.
Porsche's number 20 car, driven by Timo Bernhard, Brendon Hartley and Mark Webber, traded the lead with the number two Audi on Sunday morning, but shortly after Webber had climbed aboard the 919 Hybrid, an engine problem forced him to bring the car back into the pits, where it was retired.
That left the number two Audi in the lead ahead of the number one car. The latter car's performance was remarkable considering the car had to be completely rebuilt after Loïc Duval had an enormous accident at the Porsche Curves in practice. Duval was ruled unfit to start by Le Mans officials, and Gené was drafted in to substitute for him.
The number 14 Porsche of Romain Dumas, Neel Jani and Marc Lieb finished the race in 11th position, having been delayed by fuel flow problems in the early stages of the event and further mechanical issues in the closing stages of the event.
Victory in the LMP2 category went to the Jota Sport Zytek-Nissan of Simon Dolan, Harry Tincknell and Oliver Turvey.
Ferrari won the GTE Pro class, with the AF Corse entry of Gianmaria Bruni, Giancarlo Fisichella and Toni Vilander taking the spoils in their 458 Italia.
GTE Am fell to Aston Martin. The factory-entered car of David Heinemeier Hansson, Kristian Poulsen and Nicki Thiim was first home in their Vantage V8.