The Citizens have handed the 24-year-old centre-back, who last turned out for Maritzburg United during a loan spell last season, a life-line after spending the first half of the campaign in limbo.
The Cape-based club announced the news via their official Twitter account on Friday morning.
Mngonyama has also attracted praise from City coach Benni McCarthy, who hopes to help his new signing realise his full potential.
"When I heard there was a chance for City to land Kwanda I was instantly excited," McCarthy said in a club statement.
"Mngonyama is a soldier and probably one of the most promising defensive talents to come out of SA in a long time.
"Seeing where the club is going, building for the future, this was a key acquisition for us. I can't wait to start working with the young man and get him to where he should be."