The defending champion leap-frogged Melbourne City thanks to second-half spot-kicks from Jean Carlos Solorzano and Andrija Kaluderovic, with Central Coast remaining in eighth spot with 15 points from 17 games while Brisbane has amassed 21 from 16 matches.
It was the Mariners sixth home loss of the campaign, after just four defeats in Gosford during the previous two seasons.
Brisbane, which had only lost two of its previous 17 matches against the Mariners at this venue, has now won three games in a row.
It looked the more dangerous side early, and Solorzano had a couple of chances as the visitor looked to take the upper hand.
At the other end, Mariners new boy Fabio Ferreira had an early shout for a spot-kick denied by referee Kris Griffiths-Jones after he appeared to be upended in the box.
Mariners keeper Liam Reddy denied Thomas Broich, after gifting him possession with a misplaced clearance, while veteran midfielder John Hutchinson was unable to capitalise on a headed chance for the home side.
The Mariners suffered a big setback in the 50th minute when Eddy Bosnar was ruled to have got a hand to the ball, and up stepped Solorzano to bury the spot-kick to put the Roar in the driver's seat.
And it was unable to recover as its fading top-six prospects took a big hit.
Brisbane suffered a blow of its own when Solorzono was forced off with what looked like a hamstring strain 15 minutes from time.
But it was his replacement, Serbian import Kaluderovic, who converted a second penalty a minute into stoppage time after Anthony Kalik had tripped Broich.
Roar coach Frans Thijssen said it appeared Solorzano had suffered a hamstring tear and was facing several weeks on the sidelines.
However, he will be assessed by Roar doctors over the weekend.
"It means he will be out for some time if (he has torn his hamstring)," he said. "We have to check tomorrow.
"Hopefully, it's not too bad. It's a pity when he drops out because, at the moment, he's the one who scores the goals for us.
"Henrique will come back soon and we, of course, have the new striker (Kaluderovic) who got his first goal with a penalty, but he needs to get used to the way we play."
The match officials were booed by the Central Coast fans as they came from the pitch.
Coach Phil Moss said his side was unlucky and Bosnar's hand ball was not deserving of a penalty.
"Goals change games and that penalty was just unlucky," he said. "The first one with Bosnar has just read the flight of the ball and he's gone to put his head down because that was the flight of the ball and his arms are up to balance him.
"I don't know what you're supposed to do with your arms if you can't use them for balance."
