Cavendish had made his case for Tour de France selection after winning his second British road race title on Sunday, saying he will win stages if selected.
The 37-year-old equalled the all-time record for stage wins last year and was hopeful of breaking the record at the 1-24 July race but will be on reserve along with Florian Senechal while Julian Alaphilippe is not in the eight-man team.
Dutchman Fabio Jakobsen, who has 10 victories this year, will be Quick-Step’s sprinter.
“We have riders who can support Fabio, riders who can climb, but who can also do something in the breakaways,” said Quick-Step Alpha Vinyl sports director Tom Steels.
“Concerning our reserves, we must stress out that they showed a lot of professionalism, continued to train and remained focused in these past couple of weeks, and even brought two victories at the Nationals.”
World champion Alaphilippe said he was disappointed to miss out but understood he would not be at his best having only just returned to action following his crash at Liege-Bastogne-Liege.
“I have a natural affection for the race, from my days in the yellow jersey over the past three seasons, my stage victories and many other great memories with my team mates,” he said.
“To miss another opportunity to wear my beautiful rainbow jersey in my home country is very sad for me and I knew that this decision would be difficult for the team to take.”
The Tour begins in Copenhagen on Friday.