The Cameroon international will sign for the French Ligue 1 outfit this summer for an undisclosed fee, having made 22 appearances for Les Rouges et Noirs since joining them on loan last summer.
Makoun has struggled to hold down a place in the Villans squad and has made just seven Premier League appearances since arriving from Lyon for £6 million in January 2011.
In a statement on their official website, Aston Villa confirmed that the Cameroonian's brief stay at the club is set to come to an end.
"French Ligue 1 club Rennes will exercise their option to complete a permanent move for Jean Makoun in the summer transfer window.
"The deal for an undisclosed fee will go through on July 1."
Makoun's loan spell at Rennes was preceded by a season-long loan at Olympiakos, where he made 18 appearances and helped them win the Greek Super League.