Adelaide's Sergio Cirio scored a penalty in the 98th minute when Roar goalkeeper Michael Theo was red-carded after a brain explosion, with the match all but over.
Theo, in the act of throwing the ball out, made contact with Adelaide's Dylan McGowan, who crumbled clutching his face.
Referee Stephen Lucas sent Theo off, leaving Brisbane defender Thomas Kristensen to attempt - and fail - to keep out Cirio's match-winning penalty.
The Roar, with 33 points, remain in fourth spot on the ladder but missed an opportunity to close the gap on third-placed Melbourne City (36 points).
And Brisbane hold concerns over captain Matt McKay, who was forced from the field early in the second half with a right-knee injury.
The late drama came after Roar striker Jamie McLaren and Adelaide frontman Baba Diawara had earlier scored goals in a hard-fought game in which United playmaker Marcelo Carrusca was also sent off.
McLaren's 60th minute tap-in - his 14th goal of the league season - cancelled a neatly taken header by Diawara in the first half.
Diawara, the Sengalese striker signed by Adelaide in the January transfer window, had earlier given his new club the lead in the 16th minute before a 7,197-strong crowd.
Diawara expertly latched on to a Carrusca corner - his near-post run left Jade North lagging in his wake and he assuredly nodded into the net.
But Carrusca, arguably the most influential player on the ground, was marched in the 82nd minute - he copped an initial yellow for dissent in the first half and another for kicking the ball away after teammate Cirio gave away a foul.
Defending champions Adelaide stay in last spot but now just two points adrift of ninth-placed Central Coast Mariners.