Thom came on in the 54th minute and equalised in the 78th with a left-foot steer home.
On-field he was ruled offside, but the boot of Wanderers defender Jacob Farrell was deemed to be in line with Thom's after a three-minute VAR perusal.
The Roar are two points behind sixth-placed Central Coast, but the Mariners have two games in hand.
"It is a good story," Brisbane coach Michael Valkanis said.
"Niall came into the B team this season and he's trained a little bit with us as well. The first time I called him into the office I said, 'you are very close to travelling' and he wasn't expecting that sort of meeting.
"He went, 'what? I am travelling'. He's just got a lot of energy. He's a talented player with the potential to become a very good No.9. He gives everything. He leaves it all on the ground."
The Roar were rewarded early for going forward in waves.
Midfielder Sam Klein was heavily involved and was the provider for the fifth-minute goal to Georgios Vrakas. Vrakas linked with Klein, whose cross was not cleared by Joshua Brillante.
Vrakas, in a reflex reaction, stuck out his left foot and managed to guide the ball into the net.
The Wanderers then started to dominate possession and it was no surprise when forward Brandon Borrello scored against his old club.
Left winger Ryan Fraser landed his cross on the head of the Socceroo who was unmarked and guided it home.
Bozhidar Kraev's thunderous curling left-foot strike in first-half added time was just reward for the visitors' enterprise.
Roar goalkeeper Dean Bouzanis suffered a calf injury early in the match but battled on. At halftime he was replaced by Macklin Freke, who made a diving save in the second stanza to deny Kraev his second.
Both coaches were disappointed their sides didn't take more of the chances they created.
"We played some good footy. We created some very good moments," Wanderers coach Gary Van Egmond said after his side moved off the bottom of the table on goal difference.
"There was sustained pressure as well. You've got to ensure when you've got that momentum of putting the ball in the back of the net."
Valkanis said Brisbane had not given up on finals.
"We are not dropping tools and saying it is over. We are saying we are still in this and in the fight to make finals," he said.
13°C