According to the supersport website, the former Bafana Bafana midfielder, who is captain of Sundowns, is now tied to the club until mid-2016 when he will be 33-years-old.
Modise had been the subject of verbal abuse and the rolling of wrists from fans on Sunday as Sundowns struggled against Platinum Stars in the Nedbank Cup quarterfinal.
Spectators at Loftus Versfeld were baying for him to be substituted before Modise popped up to score the first goal of the game. He then celebrated by cupping his ear in the direction of the fans in a provocative response to their abuse.
He apologised in a statement on Tuesday for the gesture.
The club’s website said Modise admitted his response to the boo-boys after he scored was “an incident driven by high emotions, and should not have happened”.
Modise’ new contract comes as coach Pitso Mosimane has promised a major clean out at the club when the season is over.
Modise began his top flight career at Ria Stars in 2001 but the faded into the second tier at City Pillars before returning to the top flight with SuperSport United in 2006.
He moved to Orlando Pirates the next season and Mamelodi Sundowns at the start of 2011.