Aideen Keane's goal just after the hour mark and Chinaza Uchendu's double either side of Canberra midfielder Bethany Gordon's late goal proved enough for City to snag three points at Casey Fields.
City (33 points), who have three matches left, lead Adelaide (29), Wellington (28), Canberra (27), Melbourne Victory (25) and Perth (23) at the top - though the Reds and Phoenix have a game in hand.
City star and golden boot leader Holly McNamara and Canberra gun Michelle Heyman, the league's all-time leading goal scorer, were unavailable due to the Matildas' Asian Cup campaign.
For more than a half, City appeared toothless without McNamara.
Then, in the 61st minute, Keane rose highest to nod home a Deven Jackson corner against her old club.
Keane had to come off after a knock 11 minutes later.
City coach Michael Matricciani called upon Uchendu in the 83rd minute and it paid immediate dividends when the Nigerian attacker nodded home a Bryleeh Henry cross to double the hosts' lead.
Two minute's later, Sasha Grove's cross into the box caused some chaos among the City defence and Gordon toe-poked home.
But City responded almost immediately to wrap up the three points.
Uchendu latched onto Rebekah Stott's long ball, took a couple of touches then rocketed a fierce, unbeatable strike past Sally James to put an exclamation mark on the victory.
City host Adelaide on Wednesday evening, while Canberra play the Reds next Sunday.
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