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.”
A goal apiece from James Tomkins and Luka Milivojevic handed Crystal Palace a crucial 2-0 win over Huddersfield at the John Smith's Stadium on Saturday evening.
Manchester United bounced back from their Champions League exit as they beat Brighton 2-0 at Old Trafford on Saturday night to reach the FA Cup semi-finals.
Tottenham reached the FA Cup semi-finals after they cruised to a 3-0 victory over Swansea in their quarter-final clash at the Liberty Stadium on Saturday.
Premier League basement club West Brom squandered the lead as they suffered a 2-1 defeat to Bournemouth at the Vitality Stadium on Saturday.
Chesterfield boss Jack Lester felt his side were unlucky not to claim all three points after their 1-1 draw at Cheltenham.
New Swindon manager Phil Brown revelled in his side's victory at Cambridge in his first game in charge.