"I normally bounce back from crashes quite well. It's the first time in my career that I knew something was wrong," Cavendish told reporters outside the Omega Pharma team bus on Sunday morning.
"I was in pain last night but I held a bit of optimism that it was maybe just swelling and it would go down overnight, but it's actually worse this morning so it's not possible to start."
"I'm absolutely devastated by it."
Cavendish clashed with Simon Gerrans (Orica-GreenEdge) within the final 400 metres of the opening stage in Harrogate, landing heavily on his right shoulder.
Although X-rays ascertained that he had not fractured any bones, he suffered from a separated shoulder and was in too much pain to start stage two.
The latest race content, interviews, features, reviews and expert buying guides, direct to your inbox!
“I’m gutted about the crash today. It was my fault. I’ll personally apologise to Simon Gerrans as soon as I get the chance,” Cavendish said in a statement on Saturday evening.
Gerrans said on Sunday morning that he was still in pain, but that he would start the stage.
Marcel Kittel (Giant-Shimano) claimed the opening stage ahead of Peter Sagan (Cannondale), and wears the coveted yellow jersey of race leader.
Mark Cavendish announces his withdrawal from the 2014 Tour de France before stage two
