It will be the Manxman's first race since crashing out of the Tour de France during the sprint finish in Harrogate. He will be joined by Colombia's Rigoberto Uran, who will use the five-day race find his legs before leading the team at the Vuelta a España.
The Omega Pharma-Quick-Step team will also be in action in Britain this weekend at the Prudential Ride London Classic but Cavendish will not take part. Andrew Fenn, Alessandro Petacchi and Mark Renshaw have been named as the sprinters for the one-day race that finishes in the capital.
Cavendish apologized for not riding on home soil and did not say if he will go on to ride the Vuelta a España. He is on the entry list of riders submitted by the Omega Pharma-Quick-Step team for the Vuelta but any decision will only be decided after the Tour de l'Ain.
"Tour de l'Ain will be important to see where I am at with my training and recovery from my injury, and also as a bit of a test at competition pace," Cavendish said in a statement from the Belgian team.
"The rest of my program will be decided 100 percent after Tour de l'Ain depending on how I feel during that race. Together with the team we will then discuss how to approach the rest of my season."
"Unfortunately I am not able to participate in Prudential RideLondon Classic. At the moment, with the two races being so close together on the calendar, I need to focus on completing my specific block of training in Italy before returning to competition at the Tour de l'Ain shortly after. I will do my best to be there next year."
Cavendish will have the support of Julian Alaphilippe, Gianni Meersman, Pieter Serry and Carlos Verona, with Meersman a possible alternative for the sprints. It will be Uran's first race since finishing second in the Giro d'Italia in May.
"It will represent his first race in Europe since the Giro and it will be an important step to get into the rhythm of racing again after long training at altitude. It's no surprise Rigo is working in function of the Vuelta," directeur sportif Davide Bramati said.
"After this race Rigo will remain in Europe until racing begins in Spain. At Tour de l'Ain you can find a bit of everything. There will be a prologue, up and down stages for the climbers, and more. So, it's the perfect race for many riders to open up the second part of the season."