The 22-year-old sustained the injury on the weekend in a Multichoice Diski Challenge game with Golden Arrows, which ended in a goalless draw at Harry Gwala Stadium.
He joins fellow new signing Keagan Buchanan on the sidelines, with the former Kaizer Chiefs winger nursing another serious knee injury.
Farmer has only featured once as a substitute for Maritzburg's first team since his off-season arrival from SuperSport United.
He arrived at the Team of Choice carrying a knock.
Farmer struggled to secure regular game-time at Matsatsantsa following his promotion to the first side in 2015/16.