The German sprinter was visibly frustrated after feeling Cavendish had moved across his sprinting line in the final 100 metres of the finish to Villars-les-Dombes.
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Cavendish went on to win the stage, his fourth win of the Tour, while Kittel ended up in fifth place after pulling up sharply and conceding positions to Alexander Kristoff (Katusha), Peter Sagan (Tinkoff) and John Degenkolb (Giant-Alpecin).
Manxman Cavendish explained after the stage that he felt Kittel had moved off the barriers into the middle of the road and caused the coming together, with the commissaries seemingly agreeing after the stage and upholding the final result.
The German sprinter was not happy with how the day had finished, and remains on one stage win for the Tour with only one likely opportunity left in Paris on the final day.
He said he had to accept the decision, but clearly felt it was an opportunity missed after feeling good after a fairly uneventful 208km stage.
“I started my sprint with around 220 meters to go,” Kittel said, “once I was at the front I saw Cavendish come by and as soon as he passed me he went to the right.
“I had to brake and that was it. That move definitely influenced the result of today’s stage, but it’s not up to me to decide on this matter. I’m just disappointed of the outcome, because I had good sprinting legs.
“ I want to say that my team did a really good job, controlling the race, bringing me to the final and leading me out. I’m very proud of that and I want to thank the guys.
“Unfortunately, we didn’t get the result we wanted and I must admit I’m disappointed.”