Phoenix midfielder Vince Lia, who hasn't scored an A-League goal since January 23, 2011, nearly opened the scoring in the 11th minute but his right-foot strike cannoned off the post after he had driven it past Brisbane custodian Michael Theo.
The opening 10 minutes belonged to the home side but Lia's effort on goal drew the Phoenix out of their slumber as Stein Huysegems, Jason Hicks and Jeremy Brockie all had chances during the ensuing 25 minutes.
Hicks in particular should have done better when he was put through at the top of the box but Theo made a superb save to his left to deny the midfielder his first Phoenix goal.
But Wellington's dominance eventually paid off when Huysegems capitalised on a mishit shot from Brockie to beat Theo and Roar defender Jade North to the ball to bundle home a goal from close range in the 36th minute.
While the visitors deserved their lead, Brisbane came back strongly during the final five minutes of the half and Henrique should have levelled the ledger but he inexplicably misfired from inside the six-yard box with only Phoenix keeper Glen Moss to beat.
Roar midfielder Thomas Broich then hit the crossbar with a thunderbolt from distance but the Phoenix managed to hang on as they went to the sheds with a 1-0 lead.
Phoenix coach Ernie Merrick went to his bench at the start of the second spell as Leo Bertos was summoned to replace striker Tyler Boyd, which marked only the seventh appearance of the season for the All Whites utility.
Wellington's lead was eventually taken from them when 18-year-old debutant Devante Clut scored a remarkable goal in the 50th minute when his neat touch and volley gave Moss no chance.
Brisbane's goal gave them belief as they started to mount some serious pressure on Wellington, who managed to withstand the challenge through some busy defensive work and the brilliance of Moss.
Roar midfielder Dimitri Petratos had the ball in the back of the net in the 67th minute but the goal was disallowed for offside.
Wellington struggled to maintain possession during the second spell as they begun to feel the absence of Hernandez who directs so much of the Phoenix's attack from the centre of the park.
Eventually, Brisbane's weight of pressure told and when Brattan delivered his second goal of the season _ with a spectacular long-range drive _ the Roar were able to claim all three points.
Brisbane Roar 2 (Devante Clut 50, Luke Brattan 87) Wellington Phoenix 1 (Stein Huysegems 36) Halftime 0-1