Ifeanyi Eze's late strike broke a protracted deadlock in Saturday's clash at Suncorp Stadium, after James McGarry and Corban Piper had traded first-half goals.
The result puts Wellington one point shy of sixth-placed Macarthur and left 10th-placed Brisbane rueing yet another loss from a winning position.
The match had appeared destined for a draw before Eze converted his ninth goal of the season - one shy of Auckland's golden boot leader Sam Cosgrove - in the 86th minute.
Teenage substitute Luke Brooke-Smith, with just his first touch of the game, played Eze in beautifully using the outside of his right boot on the end-to-end counterattack, and the Nigerian striker made no mistake.
"This means everything for us," Eze said.
"Our main target is to get into the top six.
"Getting these three points is very important for us in achieving our goal."
The finish was frenetic - and the Roar could consider themselves unlucky - with Jordan Lauton's flying shot inside the box hitting Phoenix's Manjrekar James' forearm in the 93rd minute.
There was no whistle for a penalty, nor a VAR inspection.
Wellington were left pondering a couple of injury concerns, with Bill Tuiloma subbing out in the 62nd minute favouring a hamstring and Isaac Hughes exiting in the dying stages with his face covered in blood following a sickening clash of heads with Brisbane's Niall Thom.
Brisbane opened the scoring when Kiwi McGarry swung through a corner against his old side in the 14th minute and Wellington defended poorly on the near post.
It was McGarry's first A-League goal since 2023 and just the Roar's second from set pieces all season.
Sam Klein almost made it 2-0 when his header from a Georgios Vrakas corner was denied by the quick hands of Phoenix custodian Josh Oluwayemi.
Alex Rufer almost drew Wellington level from the edge of the box when he slammed a Kazuki Nagasawa corner into the crossbar on 32 minutes.
Then in the 36th minute, from another set piece, the Phoenix did manage to equalise in style.
Nagasawa's corner was collected by Rufer, who pushed it to Hughes, whose probing header was nodded home by Piper.
The pace slowed in the second half as the sultry conditions took their toll. Brisbane generally dominated possession, before Eze stood tall for the Nix when it counted.
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