Cavendish, 29, could not get out of the saddle for the final sprint as a result of his injuries, allowing Kittel to claim the stage win ahead of Bardiani-CSF's Nicola Ruffoni.
"I had to change my cleats in the beginning of the stage. I was coming back after and I was behind a car. Someone had to stop for a puncture so the car slammed on its brakes, and there was an island in the road. If I went right, I would hit a traffic island, so I went left and I whacked another car. I hit it with my left leg and I was down on the road," Cavendish said in a team press release.
"I still got third, but it's a shame because I really wanted to try and win in front of the British public. But accidents like this are a part of cycling and it's just a matter of bad luck. I really hope that the luck turns in the next days."
The Tour of Britain continues tomorrow with a 200-kilometre stage between Knowsley and Llandudno.