The Briton has been out of action since a bad crash in the sprint finish on stage one of the Tour de France in Harrogate last month.
Omega Pharma-QuickStep rider Cavendish suffered shoulder ligament damage in that incident, but is to make his comeback in the race in eastern France, which starts next Tuesday.
However, Cavendish will not feature in this weekend's Prudential Ride London Classic and stated that any decision on his participation in this month's Vuelta a Espana will be made 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 told Omega Pharma-QuickStep's official website.
"The rest of my program will be decided 100 per cent 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 Ride London 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."