"Due to the time of recovery needed, Cavendish will not return to competition this year," the Belgian team said in a statement.
Cavendish has had a quiet season, winning one stage on the Tour de France to take his career haul in the race to 26.
He crashed at the Tour of Britain earlier this month, choosing surgery to treat a damaged ligament on his left shoulder.
"It has been a very difficult decision," Cavendish said on the team's website, about choosing surgery.
"However, after 10 days from the crash, I still had pain and I couldn't lift or pull much weight. I tried to ride my bike a few days ago on the road, but I could not put any power out by pulling on the handlebars.
"The surgery was necessary to avoid any problems in the near future."
Cavendish will not ride in the world championships or the Tour of Abu Dhabi, both of which he said had been "important objectives" this season.
The 2011 world road champion may also have ridden his last race for Etixx-QuickStep with the transfer rumour mill linking him to the African MTN-Qhubeka team for 2016.