Mark Bridge's missed penalty proved to be costly as Frank Farina's side - who sit second in the A-League - surrendered a lead to lose for the first time against their rivals in five encounters in front of a sell-out crowd of 40,000.
Shinji Ono opened the scoring four minutes into the second half, but Bridge failed double their lead two minutes later when his poor spot-kick was kept out by Vedran Janjetovic.
That proved to be a pivotal moment, as Matthew Jurman levelled with his first goal for the Sky Blues then Richard Garcia put them in front following a mistake from captain Michael Beauchamp and Ali Abbas showed Bridge how it's done by scoring from the spot.
The victory moved the home side up to fourth in the table, just three points behind Wanderers and ensured Brisbane Roar remain seven points clear at the summit.
In the other game to be played on Saturday, Adam Taggart scored the only goal of the game in the second half as Newcastle Jets ended Melbourne Heart's seven-game unbeaten run at Hunter Stadium.
Josh Brillante was the architect, marauding forward and skipping past Aziz Behich before delivery a cross for Taggart, who finished with a half-volley.
The defeat ensured the Jets moved five points clear of their second-bottom opponents, who had won their previous five games.
