A win for the Nix would have opened up a handy four-point gap between themselves and the Roar but, instead, Wellington are now two points back and looking over their shoulders at the advancing Perth and Newcastle.
Brisbane seem to have recovered from a slump which threatened to sink their season, with this win coming on the back of an identical 2-0 triumph over leaders Central Coast.
Today, they put on a clinic in possession football in the first half, before somehow keeping a wasteful Wellington goalless in the second and landing the killer blow with 10 minutes left.
The defending champions dominated just about every aspect of the opening stanza, but they struggled to translate that superiority into an advantage on the scoreboard.
The Roar held onto the ball for more than 70 per cent of the opening 45 minutes, spent nearly two thirds of the game in the Wellington half, and looked like the side most likely to open the scoring.
But for all of Brisbane's pretty passing, the Phoenix had the better early chances. Unfortunately for the home side, both Leo Bertos and Alex Smith were guilty of squandering good opportunities and, in the 41st minute, Brisbane edged in front through the leading scorer in the league.
Erik Paartalu played a chipped pass over the Phoenix defence to the edge of the box and Berisha, allowing the ball to drop over his shoulder, spun and caught it first-time on the volley with a strike of the highest degree of difficulty.
It was the Albanian's 13th goal of the season, and it gave the visitors a slim lead to take to the break.
The Phoenix started the second spell brightest and nearly cancelled that deficit in the nascent stages, but Michael Theoklitos made a decent save to keep out Paul Ifill with the Barbados international through one-on-one.
For all their industry the Phoenix should have tested Theoklitos more than they did, but too often the final ball was lacking or players made the wrong decisions when in a position to fashion a clear-cut chance.
And, in the 80th minute, Mitch Nichols made Wellington pay for their profligacy. After receiving the ball from Ivan Franjic on the edge of the box, Nichols curled a sweet strike into the top right corner of Mark Paston's goal to secure the three points.
The Phoenix will do well to avoid dwelling on the loss too much - next week they travel to Central Coast to take on the leaders, without key men Andrew Durante and Tim Brown who will miss out through suspension.
Brisbane Roar 2 (Berisha 41, Nichols 80) Wellington Phoenix 0
