Molekwa has long served as Rise and Shine’s team manager and was elevated to the helm in March following the sudden resignation of Luc Eymael.
City have now decided to hand him the reins on a permanent basis after he led the team to sixth place in the Absa Premiership last season, the club’s highest-ever finish.
“He has now been appointed as the head coach and not acting,” club official Tincy Tema tells KickOff.com.
In the 10 league games that Molekwa was in charge of in the last third of the 2016/17 season, he won five, drew two and lost three.
Molekwa will be assisted by Phuti Mohafe, who has been working as second-in-command at Polokwane since November last year, having taken over the job from Makweni Mayala.
Modiri Marumo will remain goalkeeper coach at the club, who have so far brought in Thando Booi, Wiseman Maluleke and Ndivhuwo Ravhuhali.