The 29-year-old Cameroon international has barely figured for Villa since former boss Gerard Houllier took him to the club from Lyon in January 2011.
And, having spent last season away on loan at Greek side Olympiakos Piraeus, Villa boss Paul Lambert allowed him to join Rennes last summer.
Makoun has impressed greatly with the mid-table Ligue 1 side, who will face St Etienne in the League Cup final next month, and they have moved to tie him down to a two-year deal.
A statement on the Aston Villa website read: "Rennes will exercise their option to complete a permanent move for Jean Makoun in the summer transfer window".
It added: "The deal for an undisclosed fee will go through on 1 July."