Ovidy Karuru almost opened the scoring for Usuthu with a free header inside the box in the ninth minute but he could not find the target.
Lyle Lakay had a chance to break the deadlock in the 26th minute with a free-kick from the edge of the box but his effort sailed over the bar as City continued to push for an opener.
Thabo Nodada had a chance to give City the lead six minutes before the break after a counter-attack but he missed the target from close range as the teams entered the break scoreless.
Usuthu started the second stanza on the front foot and were threatening to get the breakthrough.
Usuthu were not to be denied on 64 minutes as Mbongeni Gumede broke the deadlock for the hosts.
Bradley Ralani had a chance to level matters for Benni McCarthy’s troops in the 75th minute after going through but he fired over the bar.
Roland Putsche fancied his chances for City five minutes before time with a long-range strike that was threatening but looped over the bar.
Usuthu defended deep in the closing minutes and managed to hold on to their slender lead to finish the 2017/18 season in eighth place.