The opening goal came with a sweet, low finish after eight minutes, while the second came in stoppage time as the visitors pushed for a winner.
Victory was the first in seven games for Usuthu. The men from Rustenburg were beaten just days after reaching the Telkom Knockout final.
AmaZulu made a superb start to the contest and went ahead with their first attack as a Njabulo Manqana corner fell to Goodman Dlamini just outside the box, with the forward crashing his first-time shot low into the bottom right corner.
A minute later, Lunga Zondi found space in a similar position, but shot straight into the arms of Siyabonga Mpontshane.
Robert Ng’ambi had Stars’ first real opening, when former Usuthu favourite Sibusiso Hadebe squared to him not long after, but the Malawian somehow missed his shot from 12 yards out as a fine opening went begging.
Ayanda Dlamini was then gifted a golden chance to double the advantage midway through the half when he dispossessed a lax Tshepo Gumede and closed in on goal, only to fire straight at the feet of Mpontshane.
At the other end, Mogakolodi Ngele had three quick chances in succession.
First, the Botswana star failed to find the target with a clear 12-yard chance after he was set up by a fine Henrico Botes first touch.
He then saw his free-kick kept out by the diving Aubrey Mathibe, before the Usuthu keeper blocked at his feet after Issa Sarr’s cross-goal effort came back off the left upright five minutes from the break.
Following that move, Manqana could have also put the hosts ahead after a flying counter-attack — the move ending with Mpontshane blocking with his fingertips leaving AmaZulu 1-0 ahead at the break.
After the restart, Craig Rosslee’s side caught the visitors on the break a number of times, but were let down by some poor decision-making in front of goal.
Dikwena had a chance of their own before the hour mark when Lindokuhle Mbatha was put through on the left by Ngele, but Mathibe did well to come off his line and block, while the rebound was also sent away for a corner.
There was another opening for Stars with 20 minutes to play as Hadebe was put through on the right, but he shot into the body of Mathibe.
With Stars pushing forward for an equaliser, Goodman Dlamini added a second goal on the counter attack when he finished with a low shot after collecting a pass from the right to seal the win.