MC Alger confirmed Mokwena's appointment in an official statement.
"Rulani Mokwena, new coach for the dean of Algerian clubs. Mokwena, welcome to Mouloudia," the club wrote.
The 38-year-old South African replaces Tunisian tactician Khaled Ben Yahia, whose short-term contract ended following the club's domestic double triumph - clinching both the league title and the Algerian Super Cup.
Mokwena returns to management after a brief spell with Moroccan giants Wydad AC, whom he joined after parting ways with Mamelodi Sundowns.
However, his tenure in Casablanca was cut short after the club failed to secure qualification for the CAF Champions League.
Despite the setback, Mokwena remained in high demand and was reportedly linked with top clubs across the continent and Middle East, including Egypt's Pyramids FC and Zamalek SC, South Africa's Orlando Pirates, Qatar's Al Shahaniya, and a Saudi Yelo League outfit.
Now at the helm of MC Alger, Mokwena will guide the club through their upcoming CAF Champions League campaign, as the Algerian giants prepare to make a return to continental football.
Last season, they reached the quarter-finals before being eliminated by Orlando Pirates.