Italian legend Alessandro Del Piero became Sydney's most prolific scorer with his early goal while Besart Berisha levelled with a first-half penalty.
But it was young midfielder Peter Triantis who sealed the win, opening his Sky Blues account with his 69th-minute strike.
The victory lifts the Sky Blues into sixth spot - the first time they've been inside the top six since round four - while Brisbane dips to eighth.
Del Piero broke the deadlock in the seventh minute when he was able to get on the end of a clever flick from Blake Powell and masterfully moved past Roar defender Ivan Franjic to score his 11th A-League goal - a record haul for a Sydney FC player in one season.
Roar's new Dutch recruit Stefan Nijland in his first start for Brisbane tried to level moments later, forcing a save from Sydney gloveman Vedran Janjetovic.
Mitch Nichols also kept Janjetovic busy with a shot from outside the box midway through the opening stanza.
But it was superboot Berisha who equalised after Roar was awarded a penalty when Sydney defender Fabio brought down Nijland in the box.
The Albanian stepped up to the mark and made no mistake, also scoring his 11th goal of the season to level at 1-1 a minute before the break.
Berisha threatened again early in the second half with a long-range effort but sent it just wide.
Sky Blues coach Frank Farina made a double substitution in the 60th minute bringing youngsters Joel Chianese and Terry Antonis on for Powell and Ali Abbas in an effort to create more pace up front.
But Brisbane continued its assault with Nijland just shaving the post.
A defensive error by late Roar substitute James Donachie gifted Sydney its second goal when his attempted clearance landed at the feet of waiting 21-year-old Triantis whose powerful strike put the host 2-1 up in the 69th minute sending the 14,589-strong crowd into a frenzy.
Del Piero almost widened the gap in the dying minutes shattering the woodwork with his spectacular free-kick.