The former Orlando Pirates and Mamelodi Sundowns coach joined the Algeria champions this season after leaving Wydad AC.
He won the 2025 Algerian Super Cup with Alger and his team are on course for another league title, in first place on the league standings with 43 points from 19 games, five points clear of second-placed CS Constantine, and with four games in hand.
But Mokwena was reportedly unhappy that he wasn't supported by the club in the recent transfer window and is now being linked with a move to Libyan giants Al Ittihad SC following Khaled Ben Yahia's recent exit.
"The decision came after the coach's meeting with the club's management, during which he expressed his conviction to end his experience with the team, after a career that lasted eight months," read part of the MC Alger statement.
“The management of MC Algeria would like to express its gratitude and appreciation to coach Rulani Mokwena and his technical staff for the work and efforts they have put forward during their supervision of the team, they wish them all the best and success.”