The two sides made two changes apiece, as Usuthu introduced Siyethemba Sithebe and Nhlanhla Vilakazi whilst City recalled Ebrahim Seedat and Kermit Erasmus.
Usuthu, who ended Mamelodi Sundowns' long-standing unbeaten run, nearly fell behind from the penalty spot following a foul on Erasmus by Mbongeni Gumede. However, the former Orlando Pirates striker saw his 12-yard effort saved by Siyabonga Mbatha.
AmaZulu soldiered on and almost took the lead when Michael Morton saw his goal-bound shot blocked by Keanu Cupido at the midway point.
In the second half, City still asked the questions and nearly received a response on 55 minutes when Teko Modise’s free-kick crashed off the crossbar.
Against the run of play, the home side went ahead through the boot of Nyongo who sent a fine curling free-kick into the top corner from 20 yards out.
McCarthy responded by introducing Surprise Ralani for Links in the final 20 minutes as the Citizens went in search of an equaliser.
However, Usuthu weren’t going to be turned over despite the late flurry from the Cape Town outfit, as they hung on to make it two wins in a row.
AmaZulu: Mbatha, M.Gumede, Sikhakhane, P.Gumede, Nyongo, Morton, Daroph, Vilakazi, Sithebe, Ncobeni, Karuru.
Subs: Boshof, Ouro-Akoriko, Van Heerden, Maduna, Chawapihwa, Ramphela, Cele.
City: Leeuwenburgh, Mkhize, Cupido, Seedat, Mngonyama, Nodada, Martin, Modise, Mokeke, Erasmus, Links.
Subs: Motloung, Putsche, Norodien, Abrahams, Roberts, Ralani.