In the 33rd minute, Roar defender James Donachie raked an Andrew Hoole cross into his own net as much of the 14,848-strong crowd groaned.
Brisbane wasted numerous chances, with Jets substitute Joseph Gibbs sealing the result in the 88th minute.
While still clear competition leaders, the Roar remain on 99 A-League wins, aiming to become the first club to reach 100.
Newcastle prevailed 2-1 against the Roar when they met on November 17 - the last time Brisbane had lost.
Newcastle have won four of their past five matches against Brisbane.
The Roar had more than 60 per cent of the possession in the first half, Ivan Franjic having the first real chance early in the match, but he became tangled with the last defender.
Seconds later, Albanian star Besart Berisha put his body on the line, colliding with Jets 'keeper Mark Birighitti in his bid to head a cross into goal.
Liam Miller missed the best chance of the first half, spraying a superb Franjic cross across the goal mouth.
Sixteen minutes in, Berisha had another header opportunity but could not control it, Franjic mirroring his efforts to nudge another cross into Birighitti's hands.
Newcastle went on some searching runs, the first genuine opportunity coming off a 27th-minute corner. The Roar's defence, which had let in just seven goals this season, held firm.
But it all came undone in the 34th minute when Donachie found his own net to hand Newcastle a 1-0 lead.
The frustration spilled into the second half as Brisbane squandered chance after chance to draw level.
Not even Henrique's injection in the 70th minute could spark the Roar, with the Brazilian missing two attempts within 10 minutes.
Brisbane went into the game without teenage tyro Kwame Yebah who is in Europe to seal a three-and-a-half year deal with German club Borussia Monchengladbach.
The 19-year-old had scored two scorching goals in three appearances for the Roar this season.
Roar coach Mike Mulvey opted not to rush experienced defender Jade North (groin) back from injury.
Newcastle were again without in-form attacker Nathan Brown and marquee player Emile Heskey through injury.
Jet Samuel Gallaway received a yellow card 21 minutes in for repeat infringements after pushing Franjic to the ground, while Roar captain Matt Smith earned a yellow for his spray after giving away a free kick.
Franjic also received a yellow close to fulltime after frustration caused him to foul Jets skipper Ruben Zadkovic.
Roar coach Mike Mulvey was left to lament the own-goal, Miller's early miss and slow ball speed.
But in the end, the wasted opportunities cost the club any chance of victory.
"We had our chances," Mulvey said.
"We just weren't incisive enough in the final third.
"It was a frustrating night for us because they got numbers behind the ball and we didn't move the ball quickly enough."
Newcastle coach Gary van Egmond praised his young charges for again shocking Brisbane, a win that could prove vital for the Jets' final standings at the end of the season.
"It keeps us in touch," he said.
"You pick up any points (you can) against Brisbane at this moment.
"There is a lot of belief in our camp.
"But if there was not that much belief in the camp before, there is now."