Khumalo made the switch to Sturrock Park in January this year, after failing to make a mark upon his return to SuperSport United last year.
The former Bafana Bafana captain saw his five-year contract with Tottenham Hotspur run out at the end of the 2015/16 season, after a number of loan spells at lower division teams.
The 29-year-old initially joined The Clever Boys on a short-term contract, with the hopes of landing a move back to Europe, but the club have since taken the option to extend his stay with the Absa Premiership title hopefuls.
