City, with captain Rebekah Stott scoring the sole goal in a win against Wellington Phoenix, jumped from seventh to fifth.
The Roar took top spot on goal difference with a classy 3-1 away triumph over Adelaide United, while Western Sydney Wanderers and Sydney FC drew 0-0 in their derby.
Melbourne City skipper Stott nodded in from close range in the 86th minute.
From a long free kick, Taylor Otto won the initial aerial contest and headed towards the goal mouth where Stott was free.
The Phoenix slipped from sixth to seventh after their first loss of the campaign.
"I'm frustrated and I think the team are," Phoenix coach Bev Priestman.
"But this game can't define us. We did a very good job against a very good Melbourne City team and now we have to grow from this."
In Adelaide, Brisbane Roar's Bente Jansen scored a brace in her side's convincing triumph - a third win in four outings.
Brisbane's Grace Kuilamu scored on the half-hour and the visitors skipped further clear when Jansen netted in the 49th minute.
But Adelaide attacker Erin Healy raised home side hopes with a 51st minute strike, only for Jansen to settle the contest with her second goal some 67 minutes in.
At Marconi Stadium, the Sydney rivals couldn't be split despite their gap on the ladder.
The Sky Blues, with two wins and three draws, sit equal top on nine points with the Roar and Melbourne Victory after the last-placed Wanderers produced a plucky display with five more shots at goal than their rivals.
In Sunday night's late clash, the Central Coast Mariners trounced Newcastle 3-1 in a derby postponed from Saturday night due extreme heat in Gosford.
21°C