City scored two goals in the space of five minutes in the first half at Porirua Park and withstood a resilient Wellington fightback to leapfrog Canberra United into first place.
One point ahead of Canberra - and with two games in hand - City will fancy their chances of widening the gap at the top of the table over the back half of the season.
City showed their quality early on Saturday with Danella Butrus in the heart of everything the premiers did right as they claimed a 16th-minute opener.
Butrus set up the goal by latching on to a Rebekah Stott ball down the left flank, racing to the byline and cutting the ball back towards the penalty spot.
Wellington's defence missed the pass completely as Leticia McKenna surged into the box and hit home to give City the lead.
City were not done there and Butrus was heavily involved once more as they added a second in the 21st minute.
After Holly McNamara made a break up the middle of the field, Butrus was found wide in space on the left and zeroed in on goal.
Her shot was deflected away by goalkeeper Victoria Esson but only as far as City's Aideen Keane, who tapped in at the back post.
Wellington rallied in the second half, with American import Makala Woods heading in an 89th-minute goal on debut.
But the Phoenix could not make the extra six minutes of added time count and find an equaliser.
City returned to the top of the table with their fourth straight win and will fancy their chances against Newcastle, who fell to a 2-1 loss against the Central Coast Mariners in Saturday's later game.
Kelli Brown put the Jets in front in the first half, before Annalise Rasmussen and Peta Trimis scored to give the Mariners the win.
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