Brisbane's 2-1 win this evening was brought about by a goal in each half with Ivan Franjic's exquisite 74th-minute winner adding to Matt Smith's effort from just before halftime.
Earlier, it looked as though Wellington may at least take a point from the game when they drew level at 1-1 via a Carlos Hernandez penalty in the 47th minute.
The first half contained missed chances at both ends with Roar striker Besart Berisha pushing a shot wide following a scramble in the box in the 18th minute.
Following that rare chance for the visitors, the home side began to take control of the game but they failed to finish.
Phoenix striker Stein Huysegems was presented with a glorious opportunity to take the lead around the 20-minute mark when he linked nicely with Hernandez but his close-range shot was well saved by Roar custodian Michael Theo.
Granted, Huysegems should have done better but his spurned chance was nothing on the clanger Jeremy Brockie delivered only six minutes later.
After Huysegems stung the palms of Theo in goal, the ball bounced to an oncoming Brockie who put his left-foot shot over the bar from only six yards out with the goal at his mercy.
Those misses eventually proved costly as Smith managed to get in behind Ben Sigmund and squeeze home the first goal of the game in the 37th minute as the Roar took an unlikely lead.
Wellington had been exposed on a handful of occasions during the first spell but Brisbane clearly didn't deserve to go to halftime with a 1-0 advantage on the scoreboard.
The Phoenix are the sort of team who look like they could do with a dose of luck and they were presented it only minutes in to the second half when referee Shaun Evans pointed to the penalty spot after Wellington midfielder Kenny Cunningham was brought down.
There didn't appear to be a heck of a lot of contact on Cunningham from Brisbane defender Jack Hingert but Evans saw enough to blow his whistle.
That gave Hernandez the opportunity to bag his first goal for the Phoenix and he made no mistake from 12 yards as he buried the ball past Theo.
The drama didn't stop there in the second spell though when Evans was back on the whistle in the 65th minute and gave Brisbane a penalty of their own after he saw Albert Riera guilty of committing a foul in the box.
Berisha, who had been off the pace most of the game, saw his spot kick brilliantly saved by Phoenix keeper Glen Moss as the home crowd found their voice.
But they were silenced when Franjic, who also got the winner two months ago, put his mark on the contest and despite a flurry of late corners, Wellington couldn't find another goal to steal a draw.
Brisbane Roar 2 (Matt Smith 37, Ivan Franjic 74)
Wellington Phoenix 1 (Carlos Hernandez 47 pen)
HT: 1-0
