Mcedi Vandala opened the scoring at the Peter Mokaba Stadium with a 34th minute penalty before Edmore Chirambadare sealed the win with his goal after 68 minutes.
The result saw Magesi move onto three points, alongside Milford, who beat City 1-0 in the opening play-off encounter.
The Citizens ended the weekend bottom of the three-team group with zero points from two games.
Magesi avoided automatic relegation on the final day of the Betway Premiership with a 1-0 defeatof Richards Bay and are now well placed to survive the play-offs, ahead of facing Milford on Wednesday.
"First and foremost, happy about the result. Happy about the two goals, happy about the performance the boys put up today. I’m quite happy about how we played," Freese said on Soccer Laduma.
“It should give us confidence going into the next game. The two goals may go a long way in this tournament. I'll have to look at how they play before we plan anything. We will also plan to go there and do well.”
