Bernhard has taken part in the last three events but is focusing on making a complete recovery after an accident in testing in March.
Audi reserve Gene will now take his place.
"I’m very pleased with the steps I’ve managed to make during this time," said Bernhard. "We’ve created a tight system of medical checks, so my progress has constantly been monitored.
"Unfortunately, there’s not enough time before the Le Mans 24 Hours to become 100 per cent fit again. Le Mans is a world-class race that doesn’t allow any compromises.
"I only want to compete at this event in perfect physical condition. That’s why on the advice of my doctors and in close coordination with Audi I decided not to run at Le Mans this year."