Brisbane striker Justin Vidic netted the opening goal in the 43rd minute and after Wellington forward Ifeanyi Eze was arguably lucky not to be sent off on the hour mark, his teammate Kazuki Nagasawa equalised in the 76th.
Wellington peppered the goal from there and recruit Carlo Armiento sent Sky Stadium into ecstasy when he lashed home a wonderful winner in the 97th minute.
The Roar haven't won in Wellington since 2017 and suffered their first defeat of the season under new manager Michael Valkanis.
Wellington got off to a bad start when New Zealand international Tim Payne was forced off with a shoulder/collarbone injury suffered in a challenge with Vidic in the 17th minute.
Payne was later seen with his left arm in a sling.
Giancarlo Italiano's Wellington had 61 per cent of first-half possession but just one shot, and none on target.
The Roar had two shots - with Sam Klein heading over the bar in the ninth minute before Vidic struck late in the half.
Brisbane's goal came when James McGarry launched a long ball forward for Vidic, who split the centre-backs then held off Manjrekar James and caressed the ball over onrushing goalkeeper Josh Oluwayemi.
Wellington lacked spark in attack and Eze arguably was unlucky to only receive a yellow card for bowling over Youstin Salas behind play.
After Eze's let-off, the Phoenix surged into the game.
Roar goalkeeper Dean Bouzanis stood tall to deny Eze's fierce near-post strike in the 62nd minute, then Phoenix skipper Alex Rufer dragged a shot wide from the subsequent corner.
Wellington hit back when Brisbane failed to clear a cross and Corban Piper burst onto the ball and squared it for Nagasawa to hammer into the roof of the net.
Armiento repeatedly attacked the Phoenix goal without reward, while Brisbane defender Hosine Bility (leg) was substituted in the 86th.
The Roar defence stood tall until, in the seventh minute of injury time, Piper won the ball and slipped it to Armiento, who rifled home across his body.
Brisbane (0-1-1) head home to host champions Melbourne City on Friday while the Phoenix (1-1-0) travel to Central Coast next Sunday.
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