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Webber, who joins Red Bull next season, failed to complete a lap after being hit from behind by German team mate Nico Rosberg.
It was the third year in a row that he had been involved in such a coming-together at Interlagos.
Brazilian Antonio Pizzonia took him out at the start last year, with Webber rejoining the race 25 laps down after the Williams mechanics had worked on the car.
In 2004, when he was at Jaguar, Webber and Austrian Christian Klien collided.
Both drivers blamed each other on Sunday.
"I braked a bit later going into turn four and then I was hit from behind," Webber said. "I lost the diffuser and that was that. It looks like Nico lost his braking point. He was very deep going into the corner and I didn't think he was going to make it.
"It's always bad when team mates collide but he didn't do it on purpose. This is the game we're in, there are no rewind buttons, so when it goes wrong it goes wrong."
Rosberg, who lost his front wing and then careered into the tyre wall in an accident that brought out the safety car, felt Webber had braked too early.
The collision ended a miserable season, their worst in 30 years, for the former champions who scored only 11 points from 18 races and finished eighth of the 11 teams.
"It can only get better from here but obviously the result is massively disappointing," Williams co-founder Patrick Head said.
"This is the second year in a row in Brazil that we've been out of the race with both cars before the end of the first lap and it is really disappointing for everyone in the team.
"We can now only go back and make sure we have a much better car and look forward to a stronger season next year."
Williams are switching to Toyota engines in 2007 and Sunday's race was a farewell for current partners Cosworth who have no team for next year.