Usuthu took an early lead courtesy of an own-goal from Mpho Mvelase, while Bongani Ndulula added the second early in the second half.
Mvelase broke the deadlock in the 6th minute as he headed the ball into his own net while attempting to clear a freekick from Marc Van Heerden.
United were then awarded a penalty in the 85th minute after Bongi Macala was adjudged to have committed a foul inside the penalty area but Mahlaba failed to capitalise as his shot was parried by Kapini.
AmaZulu finished the match strongly and had two good chances to add a third goal, but substitute John Arwuah blasted his shot over the crossbar in the 90th minute, while Ayanda Dlamini was denied by a good low save from Majola in added time.
Other Nedbank Cup Results
SWallows 4 -3 Mbombela United
Supersport United 1- 0 Amatuks
Maritsburg Utd 2-1 Blac Aces
Wits 2-0 Mabee
Pirates 3-1 Thanda Royal on Penalties