Yazid Said scored his third goal in as many games, but Melbourne Victory suffered a 4-1 loss to City in the Foxtel Y-League on Saturday.
Said struck in the second half at CB Smith Reserve to maintain his record of scoring in every game so far this season.
But Moudi Najjar's double and a brace from Connor Metcalfe saw City to its win.
Both teams had their chances in the opening stages, with Daniel Aye making a last-ditch clearance for Victory in the fourth minute.
At the other end, Said was unable to capitalise on a great opportunity as his poked effort was cleared off the line.
Stefan Ristic curled an effort over the crossbar for Victory in the 17th minute before City opened the scoring.
Victory turned possession over deep in defence, Najjar released to fire into the top corner to make it 1-0.
City doubled its lead five minutes later through Metcalfe, who capitalised on a rebound after goalkeeper Matthew Sutton made a good reflex save following a corner.
Sutton made another good stop down low to deny Stefan Colakovski early in the second half.
But the Victory goalkeeper brought down Najjar in the area soon after, the striker sending Sutton the wrong way from the penalty spot.
Victory pulled one back moments later, Said tapping in at the back post after Nicholas Sette did brilliantly down the right.
Metcalfe sealed City's win with six minutes remaining, finding the bottom corner from 20 yards.
Head coach Gareth Naven's post-match thoughts
"If you have a look at the first 20 minutes, you create opportunities because the players are performing the structure, good energy involved and they're getting rewards from it. As soon as you start to move away from those things that you do well, we start to lose those important things that help us do well in regards to creating chances and I thought that's what happened.
"It's a real slow reminder for our group that performance is everything and the ability to repeat the performance is so important. I'm looking forward to being able to help the group understand the importance of performance and repeating it and what's actually involved week in, week out in delivering that on matchday. There's some things that we're doing well, there's some things that we obviously need to get better at and that was real evident against City and some things not so good really stood out and those things we start Monday trying to get better at."
Foxtel Y-League 2018/19 Round 4
City 4 (Moudi Najjar 21'/57' pen, Connor Metcalfe 26'/84')
Melbourne Victory 1 (Yazid Said 58')
Victory: Matthew Sutton (gk); Daniel Aye (Matthew Bozinovski 46'), Benjamin Carrigan (c), Luke Goulding, So Nishikawa; Thierry Iradukunda; Brandon Lauton, Stefan Ristic (Jack Morton 64'), Aydin Mustedanagic; Yazid Said, Liston Diaz (Nicholas Sette 55').