Following a goalless first half at Cape Town Stadium, Darwin Gonzalez got to the end of a counter-attack to fire past Kaizer Chiefs goalkeeper Bruce Bvuma and give Cape Town City the lead six minutes into the second half.
It was the Venezuelan's first league goal of the season as he separated the two teams.
Chiefs were found wanting especially in the middle of the park and upfront where there was no connection between midfielders and forwards.
City technical director and head coach Muhsin Ertugral enjoyed a good day in office as he haunted his former paymasters to win 1-0 in his first PSL job in six years.
The result left Amakhosi seventh on the table while the Citizens moved one place from the 12th spot to number 11.