The Lions were leading by 17 points in the last term, but Fremantle's Michael Walters kicked a goal with two minutes remaining to put the visitors' nose in front. Fremantle won 13.16 (94) to 14.8 (92).
Walters won a free kick in a marking contest with Pearce Hanley and went back and slotted a left-footed check-side kick from the boundary line.
The Lions finished with just one man on the bench after captain Jonathan Brown (face) and utility Brent Staker (knee) were taken off in the third quarter and did not return.
Brown suffered severe facial injuries and was rushed to hospital following a sickening collision with Luke McPharlin late in the third, while Staker hobbled off just minutes earlier.
Brown was still undergoing scans post-match.
This all happened less than 10 minutes after Lions coach Michael Voss had used his substitution Amon Buchanan to replace Claye Beams.
The Lions held a deserved 10-point lead at half-time before the game changed dramatically after the break.
Fremantle started winning at the stoppages with Matthew Pavlich, David Mundy and Adam McPhee springing to life.
When Daniel Rich goaled mid way through the final term, the Lions looked home, but the dominant Aaron Sandilands, Nathan Fyfe and Walters all kicked goals to get the visitors home.
Influential players
Without good mates Luke Power (back) and Jonathan Brown (face) by his side, Brownlow medallist Simon Black was all class for the Lions. His 27 touches and nine clearances were outstanding.
What it means
While the Lions had plenty of excuses to lose, the result will not sit well with Michael Voss. They have a tough month ahead and a first-up win was crucial.
The next four
Brisbane Lions: Western Bulldogs (a), Melbourne (a), bye, St Kilda (h)
What the coach said
Michael Voss:
"I felt for most of the match, we should have won. But when you walk away from a match, you walk away with two things. Sometimes you walk away with the four points, or you walk away with the fact you're proud of what you were able to put in to the performance.
I can't fault them, I'm proud of what the guys did, they hung in there. We were courageous, but we didn't get the win. So when you fight so hard for something, it's difficult to walk away licking your wounds."
New Faces:
The Lions rolled the dice with three debutants and it came up trumps. Rowan Bewick, nephew of Essendon premiership player Darren, Ryan Lester, and Claye Beams all showed they had good futures in front of them. Beams set up a goal for captain Brown with his first touch and went on to bag one himself. Beams was a late replacement for the injured Luke Power (back) and bobbed up with two goals, while Lester also got his name on the scoreboard.
Fremantle 3.5 6.8 8.14 13.16 (94)
Brisbane Lions 4.5 8.6 10.7 14.8 (92)
GOALS
Fremantle: Mayne 2, Walters 2, Pitt, Mundy, Hill, Lower, Fyfe, Sandilands, Suban, Ballantyne, Bradley.
Brisbane Lions: Brown 3, Beams 2, Banfield 2, Rich 2, Polkinghorne, O’Brien, Bewick, Clark, Lester
BEST
Fremantle: Pavlich, Sandilands, Mundy, McPhee, Mayne, Fyfe
Brisbane Lions: Black, Leuenberger, Rich, Rockliff, Merrett, Brown, Hanley
INJURIES
Fremantle:
Brisbane Lions: Power (back, replaced in selected side by Beams), Brown (nose), Staker (ankle)
Reports: Nil
Umpires: Donlon, Stewart, Kamolins
Official crowd: 23, 373 at the Gabba
More to come
The views in this story are those of the author and not necessarily those of the clubs or the AFL