"We've chose to disqualify Peter Sagan from the Tour de France 2017 as he endangered some of his colleagues seriously in the final metres of the sprint which happened in Vittel", said the president of the race commission Philippe Marien.
In the sprint finish, Sagan veered right towards and his elbow sent Cavendish slamming into the barrier.
Race jury president Philippe Marien of the UCI says, "We have chose to disqualify Peter Sagan from the 2017 Tour de France after the tumultuous sprint here in Vittel, where he endangered several riders, including Mark Cavendish and others who involved in the crash".
Then, just before the finish line, world champion Peter Sagan appeared to knock Mark Cavendish with an extended elbow has he came out of the saddle to overtake.
He cited Article 12 of the International Cycling Union (UCI) rules, which states that any rider making a wilful obstruction "against one of the 1st 10 riders placed" faces elimination.
"If he came across that is one thing but I am not a fan of him putting his elbow out like that", Cavendish vented after the stage had finished.
He was coming from behind, I did not have time to react and go left, he said.
"A crash is a crash, I'd just like to know about the elbow really".
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"The guy on the right side, I don't know who it was, I wanted to go on his wheel, and Mark was coming from the back but I didn't already know he was behind me", Sagan said.
It came on a day when fellow British rider, yellow jersey holder Geraint Thomas, was involved in another crash at the end of what had otherwise been a fairly uneventful ride through the flatlands of the Lorraine region, from the Belgian border.
"After Richie Porte attacked I chose to go and I said to myself I was going too early", said Sagan.
However, Bora-Hansgrohe's Sagan took a second to clip his shoe back in before accelerating to outsprint Australian Michael Matthews of Team Sunweb and Ireland's Dan Martin of Quick-Step Floors. He had moved up to No. 2 on the provisional general classification, seven seconds behind Thomas, thanks to the time bonus he received for finishing second on the stage.
Thomas scraped his knee but said it was OK. "There was a crash in front of us and again I had nowhere to go".
The stage was won by French champion Arnaud Demare.
It followed an earlier pile-up toward the end of Tuesday's stage. His win allowed him to claim the sprinters' green jersey from German Marcel Kittel, victor of Sunday's second stage but who was held up by the first crash and unable to contest the sprint.
Sagan managed to stay upright and sprinted to second place, but the result was scratched soon after the stage.