Andrew Nabbout scored the game's only goal before limping off injured for Melbourne Victory who have beaten Brisbane 1-0 in their A-League clash.
Roar had 61 per cent of possession but struggled to convert it into opportunities as Roy O'Donovan's point-blank miss midway through Friday night's second half proved costly.
Brisbane were also denied a penalty approaching injury time, VAR upholding the play-on call despite replays suggesting Leigh Broxham had inadvertently handballed in the area.
"I'm happy with the way we played; the first half we started really well, created some problems for them and we can score more goals," Victory coach Marco Kurz said.
"In the second half we had luck, but we had two big chances and in the end it was a team spirit mentality to grab the three points."
It is Victory's first win after a draw and loss to start the season, but will come with headaches given Nabbout's early exit with a hamstring injury.
Captain Ola Toivonen pulled the strings for Victory, setting up the game's only goal and hitting the post himself from a set shot in the second half.
Roar defender Scott Neville somehow cleared the follow-up effort off the line, while O'Donovan was still shaking his head after his bad miss failed to reward James O'Shea's crafty run towards the box.
Earlier, Nabbout beat his man to a well-weighted Toivonen pass, flirting with a handball as he wrestled it past Roar goalkeeper Maxime Crocombe.
It was his first goal since rejoining the club after a stint in Japan, and also Victory's first this season from open play.
Nabbout's night didn't last much longer, the winger stretching for a pass and immediately grabbing at his hamstring and calling for assistance.
He attempted to play it down in a Fox Sports interview from the sidelines soon after.
But the injury, described as "serious" by his coach, is another concern given Robbie Kruse (hamstring) and Tim Hoogland (quad) are already out of action.
Many of the 12,859 fans in attendance thought the Roar would be given the chance to equalise from the spot, with Fowler saying he'd like clarification on the no-call.
"If it's (hitting the) arms in an unnatural position then it's a penalty," he said.
The loss leaves the new-look Brisbane winless after three rounds, following an opening-round draw in Perth and a second-round bye.
"We've got a few things to work on, we know that," Fowler said.
"We are a new team but we're a good team and we'll pick ourselves up and be better for this."