"You couldn't make it up," said a team spokesman after video footage circulated online of the incident late on Saturday night.
The images showed French driver Vincent Capillaire, helmeted and about to change shifts, running across to the leading Toyota as it waited for a red light to change at the pit lane exit.
Capillaire gave Toyota driver Kamui Kobayashi a thumbs-up sign, which the Japanese interpreted as a signal to go despite the light still being red.
"Drivers are told you must at all times follow the marshals," said the Toyota spokesman, who explained that Kobayashi had mistaken Capillaire for one of the officials who also wear helmets and overalls in the pitlane.
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With the team shouting at him to stop and not go out on track, Kobayashi stopped and started the car several times in the confusion. In the process, he burned out the car's clutch which led to retirement shortly afterwards.
"It would not have happened without that stop-start. He put more stress on the clutch than it would normally have encountered and destroyed it," said the spokesman.
"I don't think he (Capillaire) did it on purpose but it triggered a chain of events."
The Frenchman, who was part of the second tier Algarve Pro Racing LMP2 team, gave his version of events on his Facebook page.
"I wanted to show my encouragement to the leader car, stopped at red light a few meters in front of my box," he said. "It was a spontaneous encouragement mark as it happens between pilots.
"I was fined by stewards for this gesture and I admit it was inopportune. I regret that."
Porsche ultimately won the race with their second car that had spent well over an hour in the garage for repairs and rejoined on Saturday some 22 laps behind Kobayashi.
Toyota had another car retire after a collision while their third TS050 hybrid came home in eighth place after a long period in the garage with mechanics working on the front motor and battery.
Only one Japanese manufacturer has ever won Le Mans, Mazda in 1991. Toyota have been five times runners-up and have spent hundreds of millions of dollars over the years in pursuit of victory at the French endurance classic.
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
