The inaugural women's Distance Derby on Monday took place on neutral territory at Wanderers Football Park at Blacktown in western Sydney between two sides forced to relocate because of COVID-19 issues.
Perth didn't win a game last season, but back-to-back victories have propelled them above Melbourne Victory into fourth spot, though the latter are just a point behind with two games in hand.
Last-placed Wellington, who have now lost eight straight since drawing their first game, came from 1-0 down to lead 2-1 at halftime.
Perth substitute and American import Cyera Hintzen headed a close-range equaliser in the 81st minute and seven minutes later passed to Danish international Mie Leth Jans, who tapped in the winner.
Phoenix had a chance to equalise in added time, but Grace Wisnewski's close-range attempt lacked the power to beat Perth goalkeeper Morgan Aquino.
"I think the first half we didn't have the performance we were after, Phoenix came up with a lot of high pressure which we had to deal with," Perth defender Elizabeth Anton said.
"We did try and solve that In the second half, but the main thing was we needed to fight more and show our resilience come through and our fight, which I think we did."
Perth opened the scoring in the 14th minute when a Sofia Sakalis cross from the left deflected off Phoenix defender Kate Taylor past her own goalkeeper.
Wellington equalised six minutes later after Alyssa Whinham's delightful through-ball was struck hard by Grace Jale, with Aquino getting her hand to the shot but unable to keep it out of the net.
There was a far worse moment for Aquino five minutes later when she rolled the ball out of her penalty area.
Wellington's Chloe Knott came charging in and pounced on the ball and slid it across Aquino into the far corner.
Perth lifted their intensity after halftime and regained control.
"I felt we got to that mindset of defending the win rather than kind of sticking to our own game," Phoenix coach Gemma Lewis said.
"At 2-1 you can't spend 45 minutes trying to defend a lead so I think that's probably where we went wrong a little bit."
Before the game, Phoenix revealed three players, Isabel Gomez, Te Reremoana Walker and Jordan Jasnos weren't considered for starting selection because of disciplinary reasons,
Gomez, who was chosen on the bench so Wellington could field a squad of 16, came on after halftime.
Lewis didn't want to disclose exact details of what the players had done, but said it was a COVID-19 breach.
"It was a little bit of learning from them in terms of they weren't kind of putting the team first or behaving in the way of a professional athlete in terms of the choices they were making," Lewis said.
The trio will be available for the next game.
Perth halftime substitute Gemma Craine suffered a suspected broken wrist late in the game.
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