The 25-year-old looked set to join Liverpool last summer for £53m before negotiations between the clubs ended.
It was reported elsewhere that Fekir had undergone a medical and agreed personal terms, only for the deal not to be completed.
But, with 12 months remaining on his contract at Lyon, Aulas says the club intend to cash-in on the France international ahead of next season.
Following Friday's 3-2 victory over Nimes, Aulas said: "Effectively, Nabil is outside [of the two departures expected], because we have an understanding that he can go.
"Thanks Nabil for bringing what he brought, we have an understanding to let him go.