Porsche drivers Marc Lieb, Neel Jani and Romain Dumas arrived at Le Mans leading the Drivers' Championship with 43 points, 18 ahead of the Audi trio of Loïc Duval, Lucas di Grassi and Oliver Jarvis. Toyota's Kamui Kobayashi, Mike Conway and Stéphane Sarrazin occupied third. In the Manufacturers' Championship, Porsche led with 55 points over Toyota and Audi.
A scheduling conflict with the 2016 European Grand Prix meant reigning champion Nico Hülkenberg could not defend his title. The ACO expanded the entry to 60 cars, up from the usual 56, and made circuit changes at the Porsche Curves, installing SAFER barriers at a turn that had caused a serious accident during 2014 practice.
Heavy rain in the hour before the flag fell forced the organisers to start the race behind the safety car for the first time in Le Mans history. Actor Brad Pitt waved the French tricolour at 15:00 CEST. Once the track dried after 53 minutes, the safety car peeled in and Jani retained his pole advantage.
Toyota, Audi and Porsche traded the lead through the opening stint. Kobayashi's No. 6 Toyota eventually established a commanding front-running pace, helped by a turbocharger failure that dropped Lotterer's Audi from contention. Hartley's No. 1 Porsche lost two and a half hours in the garage with water pump and engine temperature problems, falling to 53rd.
As night fell the battle distilled into a contest between both Toyotas and Jani's No. 2 Porsche. Conway and later Sarrazin led for Toyota while Jani, lapping more than a second faster than teammate Bernhard, overtook him on lap 120. Multiple slow-zone procedures and four safety car deployments compressed the field at various points without breaking the pattern at the front.
By morning the two Toyotas had opened a significant lead over the Porsche. Davidson and Nakajima in the No. 5 Toyota could not be matched for pace by Jani, who found his long-race speed advantage gradually nullified.
With six minutes remaining, Nakajima held a 70-second lead over Jani and appeared set to hand Toyota its first overall Le Mans win. The No. 5 car then slowed dramatically on the Mulsanne Straight, a failure of the connector line linking the turbocharger to the intercooler stripping the engine of power. Nakajima crossed the start-finish line and stopped. Jani, now closing at full speed, caught and passed the stranded Toyota on the final lap to take the chequered flag.
It was Jani and Marc Lieb's first Le Mans victory and Romain Dumas' second, his first coming in 2010. The sister No. 6 Toyota of Sarrazin, Conway and Kobayashi finished three laps behind in second, while the No. 8 Audi of Duval, di Grassi and Jarvis completed the podium, preserving Audi's record of having a car on the Le Mans podium every year since its debut in 1999.
The ACO subsequently amended its regulations: instead of the flat six-minute tolerance on the final lap, penalties would be applied on a sliding scale for any lap exceeding six minutes, and any car unable to complete the final lap in under fifteen minutes would no longer be classified.
On the precise fiftieth anniversary of Ford's first overall Le Mans victory — when the blue oval swept the podium in 1966 with the GT40 Mk.II — the new Ford GT of Joey Hand, Sébastien Bourdais and Dirk Müller won the LMGTE Pro class. The No. 68 American entry led all but 26 laps of the race in company with the Risi Competizione Ferrari 488 GTE of Giancarlo Fisichella, Toni Vilander and Matteo Malucelli.
Post-race, the No. 68 Ford was penalised a total of 70 seconds for speeding in a slow zone and for faulty wheel speed sensors; Risi's Ferrari received an additional 20 seconds for ignoring black-flag-with-orange-disc signals. After penalties, the Ford's margin of victory over the Ferrari was reduced to 10.2 seconds. Ford Chip Ganassi Racing USA's sister No. 69 car of Ryan Briscoe, Scott Dixon and Richard Westbrook completed the LMGTE Pro podium.
The Signatech Alpine-Nissan of Gustavo Menezes, Nicolas Lapierre and Stéphane Richelmi won LMP2 after leading the final 196 laps, earning Lapierre his second consecutive class victory. The G-Drive Racing Oreca of Roman Rusinov, René Rast and Will Stevens finished on the same lap in second.
In LMGTE Am, Scuderia Corsa's Townsend Bell, Jeff Segal and Bill Sweedler won in a Ferrari, edging out the AF Corse Ferrari of Emmanuel Collard, Rui Águas and François Perrodo. Khaled Al Qubaisi, Patrick Long and David Heinemeier Hansson were third for Abu Dhabi-Proton.
The 2016 race entered Le Mans legend through two narrative threads: the improbable mechanical failure that denied Toyota victory within sight of the flag, echoing similar misfortunes that had haunted the team at the circuit, and the symmetry of Ford's class win on the golden anniversary of its 1966 triumph. The ACO's regulatory response to the final-lap drama — creating a graduated time-penalty scale — reformed the rules governing finishing conditions for all subsequent editions.