Mitch Nicholls put Brisbane ahead in the first half, but goals from Mark Bridge and Youssouf Hersi in the second half gave the Wanderers the three points.
The Roar took a deserved lead after 21 minutes when the ball fell to Nicholls who found the right angle to beat goalkeeper Ante Covic.
Bridge netted the equaliser after being set up by Jerome Polenz on the edge of the area.
Hersi was then allowed to race through to collect a Dino Kresinger header before scoring from close range.
Having taken the lead in the first half the Roar, the reigning A-League champions, ended the game with a third straight defeat to lie in the bottom two, with the Wanderers fourth in the table.