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.
SIGNING ALERT!
— Cape Town City FC (@CapeTownCityFC) December 29, 2017
City is delighted to announce the acquisition of Kwanda Mngonyama from Mamelodi Sundowns for an undisclosed fee. #iamCityFC #FutureIsNow pic.twitter.com/sfYUERU1c3
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."