He dislocated his shoulder following a collision with Simon Gerrans shortly before the finish line in Harrogate.
Although he had hoped to ride today, he has now been ruled out of the remainder of the Tour, and is expected to undergo an operation that may also rule him out of the forthcoming Commonwealth Games.
Cavendish clashed with Australian Gerrans as both riders came down hard in the final 200 metres of the 190.5km stage from Leeds.
Cheered on by the fans of his mother's home town, Cavendish crossed the finish line clutching his shoulder, in tears and wincing in pain.
The Manxman later admitted that the crash was his fault.
"I'm gutted about the crash today,” Cavendish said. "It was my fault. I'll personally apologise to Simon Gerrans as soon as I get the chance.
"In reality, I tried to find a gap that wasn't really there. I wanted to win today, I felt really strong and was in a great position to contest the sprint thanks to the unbelievable efforts of my team.
"Sorry to all the fans that came out to support - it was truly incredible.”
He spoke to the media again before Sunday's second stage, adding: "When I got on my bike after my crash yesterday it wasn't possible to hold my handlebars. When I took my skinsuit off I saw there was something wrong with my shoulder. It was sticking out a bit like it shouldn't.
"So we went to get it checked up and I was in a lot of pain. I couldn't move my shoulder. I held a bit of optimism that maybe it was just swelling and it would go down a bit this morning, but it's actually worse this morning.
"I can't move my arm. I'm gutted, I'm majorly disappointed, but it could be worse."
- Sports & Recreation
- Simon Gerrans