Bereft of star power with seven suspensions and a further two injuries to senior players, City looked gone for all money when Jamie Maclaren put his side two up by half-time.
But Bruce Kamau's deflected strike and Nicolas Colazo's penalty gave City a share of the points against the odds.
It was spirited and it might just be a comeback that ignites City's spluttering season.
For Brisbane, there will be disappointment at blowing a two-goal lead, but the result preserves their hold on third place after a challenging week of their own.
Coach John Aloisi made six changes from the side who stunned ultra-rich Shanghai Shenhua mid-week to qualify for the Asian Champions League.
Maclaren was one of those to back up his effort, and put Brisbane ahead from the spot on 33 minutes.
Referee Alan Milliner awarded a soft-as-butter penalty for Josh Rose's shirt-tug on Brandon Borello, allowing the Socceroo to beat recalled goalkeeper Thomas Sorensen.
In first-half stoppage time, Maclaren made it two after latching onto Manuel Arana's through-pass and rolling the ball inside the far post.
A week after their controversial derby defeat, City players raged once more against a possible offside but replays showed the 23-year-old to be in line with City's Ruon Tongyik.
With a half to reduce the deficit - unlike their derby capitulation - City went to work.
Kamau scored his first goal in a City shirt when he drilled a deflected effort past Michael Theo on 58 minutes.
City had their equaliser after Milliner squared-up his first-half penalty decision with one against Brisbane.
Nick Fitzgerald ran at Roar's 17-year-old debutant Dane Ingham and Milliner awarded a similarly soft penalty after seeing a light shirt-pull.
Brisbane finished the stronger but couldn't find a winner, partially due to Sorensen.
The Dane was warmly applauded with his first touch of the ball and produced a string of crucial saves through the match.
The 40-year-old rushed well outside his box to stop Borello's breakaway effort, before denying Maclaren a hat-trick from close range.
Two City debutants also impressed.
Right-back Dylan Pierias, 16, became the A-League's first player born this century, and Denis Genreau, 17, was busy in midfield on his first start.