After falling behind in just the second minute, fit-again centre back Kate Taylor drew the Nix level shortly before halftime.
Ava Pritchard gave Wellington the lead in the 74th minute with a quality first-time strike, before fellow forward Grace Jale scored her fifth goal of the season in second-half stoppage time to secure the three points.
Western Sydney scored from virtually the last kick of the game to complete the scoring.
“It was good to finally get the game underway to be honest. There were a lot of postponements and a lot of things changing,” Phoenix head coach Gemma Lewis said.
“It took us a bit to warm into the game and we probably conceded the last goal because we were pushing for another one for goal difference,” Lewis said.
“That just shows how hungry the girls are to want to try to get off the bottom of the table that even when they’re 3-1 up straight away they were saying ‘let’s get another one, let’s get the three goal difference to try and take us off the bottom’.
“The positive mentality from them is quite cool to see.”
Lewis made three changes to the XI which started Wellington’s last match against Adelaide United, with club captain Lily Alfeld and Taylor back from international duty and injury respectively.
Alfeld returned in goal in place of Brianna Edwards, while Te Reremoana Walker made way for Taylor at the heart of the Phoenix defence.
Hannah Jones was also reinstated in midfield in place of Grace Wisnewski, who has returned to New Zealand for mental health reasons.
Forward Kelli Brown was named on the bench, included in the matchday squad for the first time since the middle of January after being forced to sit out their last six games with concussion.
The Wellington Phoenix will have a chance to move off the bottom of the table on Friday evening when they will bring down the curtain on their maiden season against Perth Glory at WIN Stadium in Wollongong.
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