The Citizens came into the promotion play-off encounter needing a victory to still have an opportunity to play Betway Premiership football in the next campaign.
The hosts started strongly, having most of the possession in the first half and pegging Magesi back but the break through never came until two minutes before halftime.
Therlo Moosa was on hand to apply the finish fro close-range after from a rebound after City engineered a well-worked passing move.
Magesi, who finished 15th in the Betway Premiership, drew level early in the second half when Mcedi Vandala rounded home goalkeeper Luca Diana-Oliaro before finding the back of the net.
City appeared to take a serious knock after conceding and, although they still remained in control of possession, did not create enough going forward to trouble the visiting defence.
Magesi, on the other hand, used what little they saw of the ball to take a more direct route and almost caught the home side out on a few occasions.
City came close to finding a winner deep into eight minutes of injury-time but the ball rattled the cross-bar as Magesi survived and live to fight another day to retain their top-flight status.