The 38-year-old Australian's Porsche 911 made contact with Matteo Cressoni's Ferrari on the final corner of the six-hour race in Sao Paulo and slammed into a track barrier.
Webber, quit Formula One last year, was not seriously hurt, according to a statement on the Endurance Series website (www.fiawec.com).
A subsequent statement on Webber's official Facebook page said he was OK and had been taken for medical checks.
"After his accident in the six hour race in Sao Paulo, Mark is awake and alert," the statement said. "(He) has been taken to the medical center for further checks."
After a 12-year career in Formula 1, former Red Bull driver Webber joined the Porsche team in the Endurance series where he finished ninth overall.
