Western Sydney made a fast start to the match, earning a two-goal advantage within the first 10 minutes.
In the fourth minute, Gabriel Cleur profited from the aftermath of a corner to stab the ball in from point-blank range.
Four minutes later, a neat right-sided move concluded with the ball at Alexander Badolato’s feet. The 19-year-old kept his composure and blasted a strike into the roof of the net.
Western Sydney went into the break with their commanding lead intact.
However, City halved the deficit in the 78th minute when Noah Maieroni’s volley from the edge of the box took a deflection and spun into the right of the goal.
City’s pressure continued into stoppage time, and a couple of late chances came close to getting them on level terms.
Lawrence Thomas was equal to the challenge and the Wanderers held on to book their place in the next round.