Although Mark Cavendish was the talk of stage 14, Briton Chris Froome maintained his overall lead and remains favored to win the Tour de France.
Cavendish insisted his sprint was clean, even if Kittel had a slightly different point of view.
World champion and green jersey holder Peter Sagan (Tinkoff) finished strongly to take third place while German Kittel finished fifth, protesting as he felt Cavendish had veered towards him during the sprint for the line.
The German was unhappy that his British rival seemed to swerve in front of him in the finishing straight, but the race jury decided Cavendish had done nothing wrong.
Mark Cavendish is determined to make the most of his winning form by riding through the Alps and securing a stage win on the Champs Élysées on Sunday. Reinardt messed up a bit - I was on Kittel and he brought the other trains past, and I thought, oh this is it, it's finished. Following my instinct, I would have jumped earlier, but when I saw Marcel Kittel taking the lead with only four guys 2km before the end, I understood it would kill him ultimately.
Should he win both, he will move on to 32 Tour career stage victories and to within two of Eddy Merckx's all-time record of 34.
"I just wanted to get a feeling for how the group was, and who was reacting and who to look out for", Froome said. I think people are expecting more fire and fight from us.
"Cavendish is really aero and fast, so I knew that he would be hard to beat today", he said.
But there has been a worrying trend for those seeking drama and excitement in this race, and that's been the outright domination of Froome's Sky team. Monday in Bern is not an easy sprint, but it's a sprint and it's Nelson Mandela Day, so it's a big thing for the team. I've been refreshed by riding on the track again, but the key point is that I'm more patient than past year.
As France began three days of national mourning, there was a minute's silence prior to the start of the stage to honour the victims of Thursday's terrorist attack in Nice.
Dutchman Bauke Mollema remains second at 1min 47sec with another Brit, Adam Yates, third at 2:45. A four-rider break: Cesare Benedetti (Bora-Argon 18, ) Jérémy Roy (FDJ, ) Alex Howes (Cannondale-Drapac, ) Martin Elmiger (IAM Cycling) stayed away until the final 14 km when Howse dropped.