Usuthu took aim at the NFD outfit, who have already tasted Premiership blood by knocking out Polokwane City in the first round.
The top-tier side were given an early shock as they fell behind in the seventh minute with a header from Clint Fredericks at the far post.
This surprise setback pushed them forward and they broke free on the right with Jabulani Ncobeni on a counter-attack but the midfielder was unable to find the equaliser minutes later.
It got worse for Usuthu when they succumbed to a second goal after Duncan Adonis turned from provider to finisher with a low shot that beat Baolefa Pule after 25 minutes.
Pressure began to take its toll on the home side, who looked to pull one back before the half-time break, but were unable to break down the opposing defence.
Ubuntu continued the scoring spree in the second half with their third from the boot of Kamohelo Mahlatsi, who poked home on the second attempt after mis-kicking the initial effort from a cross.
The hosts eventually pulled a goal back with a glancing header from substitute Mabhuti Khenyeza 15 minutes to full time.
Then the post on two occasions denied them a second goal, first with a shot from Ncobeni followed by a header from Augustine Ramphele.
AmaZulu threatened for a comeback after Ovidy Karuru headed in their second from a cross on the left in added time, but they were unable to bag a third as Ubuntu held on for the win.
AmaZulu: Pule, P. Gumede, Mabiliso, Nyongo, M. Gumede, Morton, Ncube, Ncobeni, Cele, Kararu, Manzini.
Subs: Murambadoro, Mthembu, Sikhakhane, Lumkwana, Maduna, Ramphele, Khenyeza.
Ubuntu: Khoza, Sigwebela, Heutchou-Kuilong, Gwala, Bezuidenhout, Chiwunga, Donn, Fredericks, Adonis, Mahlatsi, Cale.
Subs: Jacobs, Isaacs, Mayo, Sampson, Madikane, Sibanda, Sefoli.