Back-to-back-to-back MTN8 champions Orlando Pirates came into the match on Saturday as favourites having gone 11 matches across all competitions without tasting defeat.
The noisy home crowd at Orlando Stadium was silenced in the 32nd minute when Delano Abrahams headed in a Godfrey Mashigo cross past Sipho Chaine to give Magesi FC a 1-0 lead.
In the 39th minute, it was 2-0 after Thabiso Sesane deflected the ball into his own net after failure by defenders to clear the ball from the danger zone.
It got worse for Sesane when he conceded a penalty in the fourth minute of added time with a foul in the danger zone. Chaine denied Edmore Chirambadare from 12 yards, but the rebound fell kindly to the latter who made it 3-0.
Kabelo Dlamini gave the Soweto giants hope with a brilliant strike from the edge of the box after Deon Hotto set him up in the 85th minute.
Three minutes later, a deflected Evidence Makgopa effort made it 3-2 to bring the crown at Orlando to life. In the final minute of added time, Mohau Nkota thought he had leveled matters only to be stopped by the referee's offside call and Magesi held on to secure a 3-2 win.