The physical contest hit boiling point as Brisbane tried to chase down Max Caputo's 11th-minute header.
A shoving match between the two sides broke out in stoppage time, which was followed by the visitors having a second appeal for a handball penalty being turned down.
The ill-feeling continued after referee Tim Danaskos signalled full-time, as Roar coach Michael Valkanis remonstrated with the official and City chief executive Brad Rowse and players and staff from both sides appeared to angrily clash on the field and in the tunnel.
But both City boss Aurelio Vidmar and Valkanis, who was only just returning from a red card suspension on Tuesday, played down any post-game ill-feeling, with the latter also hesitant to comment on his side's penalty appeals.
"I don't think there was so much going on," said Valkanis.
"I think we were all giving handshakes to each other and saying, well done and well fought."
Vidmar also rubbished suggestions that anything during the game crossed a line.
"There's always going to be (physicality)," said the coach.
"You've got to have rocks in your head if you don't want to be a physical team – everyone is physical."
Last having saluted on December 6, City gained an important win, with the three points moving them to fifth on the table.
Playing the third of four games in 10 days, the Roar missed the chance to go top for a second-straight game, with a tough task now awaiting them when they host league leaders Auckland on Friday.
Valkanis signalled they'd be without Jay O'Shae for that fixture, after the skipper was forced off with an ankle injury.
"We've taken some heavy knocks today in the game," he said.
Caputo took advantage of Brisbane keeper Dean Bouzanis flapping at an Emin Durakovic corner to nod home early, with City contentiously denied a second in the 43rd minute when Andreas Kuen's blast was disallowed for a foul called against Nathaniel Atkinson.
Roar improved in the second half, but Georgios Vrakas' 50th-minute shot proved their only one on target, with Bouzanis - bandaged after having his nose smashed - repeatedly called into action late and Andrew Nabbout hitting the bar in the 86th minute.
