The German had looked ill at ease since Friday practice on the new Istanbul circuit and was in 10th place when he and the Australian tangled on lap 15 of the 58-lap race.
Webber, who had been running as high as sixth, was a lap down after pitting for a puncture and he tried to squeeze past on the final corner at the end of the back straight.
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The seven times champion, 32 points beind championship leader Fernando Alonso with five races remaining after Turkey, rejoined the race in 19th position. He came in again after one lap and retired.
Webber followed him back to the pits after another rear wheel puncture ended his race.
