The team stated, "it was confirmed that all ligaments around the AC-joint were ruptured and the shoulder separated," and said the surgery will take place on July 9.
Cavendish will be out of competition for at least six weeks while he rehabilitates his injuries.
"It's worse than I was hoping, but immediately after the crash I knew something was really wrong," Cavendish said. "It is really painful, but at the moment all I can do is focus 100 per cent of my effort on my recovery to be able to get back racing for Omega Pharma - Quick-Step as quickly as possible."
Cavendish collided with Simon Gerrans in the final meters of the sprint on stage 1, as both riders battled for the wheel of Peter Sagan in hopes of winning the first yellow jersey of the Tour de France.
Cavendish took responsibility for the incident, saying "I wanted it that bad and I tried to find a gap that wasn't there. I spoke to Simon after the stage, I asked if he was OK, and I also spoke to him on the phone later and apologized to him. I really hope he's OK and today's a good stage for him. I wish him a good rest of the Tour."
It was clear after Cavendish dusted himself off that something was very wrong with his 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."