Webber's Porsche 911 made contact with Matteo Cressoni's Ferrari on the final corner of the six-hour race in Sao Paulo, slammed into a track barrier and burst into flames.
The impact destroyed his prototype Porsche and he was photographed giving the thumbs-up as he was removed by stretcher. Both cars were totalled.
WEBBER TAKEN TO HOSPITAL
Webber, who quit F1 in 2013, was not seriously hurt, according to a statement on the Endurance Series website. A subsequent statement on Webber's Facebook page said he was OK and had been taken for medical checks.
The statement added: "Mark is awake and alert after his accident in the six-hour race in Sao Paulo. He was taken to the medical centre for further checks."
A team mate, Romain Dumas, was quoted by Fairfax Media: "He was talking on the radio. He knows his name, he knows where he is, it looks OK."
Commentary on a video of the incident reported that he was stretchered off the track but was saving one arm at the crowd.
Video: Webber crashes in WEC race in Brazil
Webber's 12-year career in F1 ended as a driver for the Red Bull F1 team. He joined the Porsche team in the Endurance series where he finished ninth overall.
Meanwhile, also in Brazil, another F1 veteran Rubens Barrichello on Sunday secured the Brazilian stock car championship in Curitiba.