The Phoenix's inability to convert chances at Porirua Park on Sunday eventually came back to bite them with the Wanderers' Chinese import Yuan Cong scoring the decisive goal in the 78th minute.
Yuan's first effort was saved by Victoria Esson before she fired in the rebound for a victory that has major ramifications for the make-up of the final regular-season table with one round left to play.
Western Sydney climbed off bottom spot with the win, heaping the pressure on bitter rivals Sydney FC to get a result against Central Coast next week to avoid their first wooden spoon.
Cong's goal also killed off the Phoenix's distant hopes of pipping City to first spot.
Bev Priestman's side came into the game needing to win to keep their hopes of a first-placed finish alive, but they were wasteful in front of goal.
Pia Vlok had two good chances in the first half and Makala Woods was denied by Sham Khamis prior to Cong hitting the winner.
"I'm really disappointed but the one thing I would say is adversity is good for you," Priestman said.
"You don't choose when it hits you and now is the time to react to adversity.
"I don't think it was our best version of ourselves but I think we gave them that goal and then we were on an uphill climb."
Wellington remain second (31 points) but their hopes of clinging on to that spot and avoiding an elimination final will come down to the final round of the season when they face fourth-placed Adelaide United (30 points).
Canberra United, who sit third, are level on points with Wellington but with an inferior goal difference after playing out a 0-0 draw with the Mariners in Sunday's other game.
Central Coast can lock up a top-six finish with victory over Sydney.
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