"It's devastating," said Cavendish, who will have an MRI scan on a dislocated shoulder and torn ligaments.
As for the Omega Pharma - Quick-Step rider's hopes of competing for the Isle of Man at the Commonwealth Games, it was reported that he is considered by his team to be "very likely" to need surgery, which would rule him out of Glasgow.
Cavendish, aiming for a 26th Tour de France stage victory and the yellow jersey he has never won, dislocated his right shoulder in the finale of the opening stage from Leeds to Harrogate, his mother's hometown.
The 29-year-old had appeared too eager to succeed in the closing stages and, using his shoulders for leverage to prevent being squeezed for room, swayed towards Australian Simon Gerrans, bringing down both of them. German Marcel Kittel narrowly avoided the carnage and sprinted clear of the pack to claim the overall leader's yellow jersey following his fifth stage win overall.
"Normally I bounce well when I crash but when I was on the floor I knew something was wrong. For the first time in my career I knew something was wrong. I wanted to cross the finish line as it was in Harrogate, I got back on the bike but couldn't hold the handlebars. When I took my skin suit off my shoulder was sticking out the way it shouldn't," said Cavendish, who had won at least a stage in every Tour since 2008.
"I had held some optimism that it would just be swelling but this morning was worse. I'm gutted and majorly disappointed. I had really wanted to win for all the people watching."
Team doctor Helge Riepenhof said Cavendish's reaction in the hours after the crash was that he wanted to be at the start yesterday.
"With things like this Mark needs some time to be convinced that he has no chance to ride," he added.
OPQS's start to the Tour was described as a "nightmare" by team manager Patrick Lefevere, who appeared to suggest that Gerrans had been slightly to blame for the crash.
"Gerrans came a little bit quicker but he was next to Mark. He was at the end of his sprint and tried to go in Mark's slipstream and he used his elbow to break down Mark. Mark used his body against him and the rest is what we saw," the Belgian said.
Cavendish, however, explained it had been a racing accident and said he had apologised to Gerrans. "The two of us were on Peter Sagan's wheel. I wanted to go but Gerrans was there. I wasn't budging and Simon wasn't budging and we went down."
OPQS suffered more misfortune when Italian sprinter Alessandro Petacchi suffered an allergic reaction to a bee sting. "We could give him antihistamine but that makes you rather tired," Riepenhof said.