City are now without a head coach following the sudden resignation of Luc Eymael, who has since joined Bloemfontein Celtic.
Mohafe was working as an assistant to Eymael since November last year having taken over the job from Makweni Mayala, who had been the second in command through the period since Selaotse Mosala left.
He has previously worked at Witbank Spurs and Cape Town All Stars.
Molekwa – who KickOff.com spoke to – has been with the club for several years working as a team manager while doubling up as assistant coach.
Retired goalkeeper Modiri Marumo remains the keeper coach.