An early penalty from Roar attacker Henrique – his sixth goal of the season – proved the difference in front of more than 10,000 fans at a rain-soaked Pirtek Stadium.
The defeat means the Wanderers – crowned kings of Asia just over a month ago – are still without a win after eight games and remain bottom.
Brisbane, meanwhile, have now secured a draw and a win under new boss Frans Thijssen to jump up into the top six for the first time this season.
The visitors were awarded a fifth-minute spot-kick when Mensur Kurtishi was brought down in the box by Seyi Adeleke. Henrique stepped up, sending the resulting penalty straight down the middle past a diving Ante Covic.
There was late drama when substitute Nikita Rukavytsya was denied an equaliser in stoppage time by the frame of the goal.
Winger Rukavytsya picked up the ball just outside the box and went on a slalom run past three Roar defenders before unleashing a shot onto the crossbar and over.
