The scores were level at half-time, but substitute Lisa De Vanna scored the winner midway through the second half.
The Roar gained revenge for last year's result which saw the Sky Blues triumph 3-2 in the title decider.
"Credit to the girls, they stuck with it, put their bodies on the line and got their reward in the end," said Brisbane Roar coach Jeff Hopkins.
"The game at the beginning of the season (4-2 defeat) gave us a wake-up call. We have worked on a number of things week by week since then and I thought our performance today defensively and also going forward was one of our best of the season."
Roar captain Clare Polkinghorne said the team's gameplan came off.
"Our key focus was to start well and not let them get any momentum, and the early goal was a bonus," she said.
"It all came together for us today, we were completing passes and doing well in the final third which has been our problem lately."