Fremantle led by 17 points late in the game and were on course for a maiden premiership when Brisbane burst to life and Logan Morris put the Lions in front with a minute left, then kicked the sealer.
In prevailing 14.12 (96) to 12.17 (89) in front of 100,023 fans at the MCG, the Lions joined Hawthorn (2013-15) and the legendary Brisbane team of 2001-03 as the only sides to win three premierships in a row this century.
Brisbane also became only the second team, after Melbourne, to pull off two VFL/AFL premiership three-peats.
The Lions somehow kicked the last four goals of the match.
"If I was being completely honest, you guys probably deserved to win the game today," Brisbane coach Chris Fagan told Fremantle in the post-game presentations.
"But my boys they've got a stack of heart and they know how to fight their way right to the end ... and now we've got three premierships in a row to show for it."
Fremantle skipper Alex Pearce suffered a devastating Achilles injury that ruled him out of the game in the third quarter.
The Dockers pulled the trigger on their "Wharfie Time'' crowd activation when Patrick Voss put them up by 17 points.
Then, improbably, Brisbane reeled them in, delivering Fagan a third premiership amid heavy speculation it was his final game at the helm.
Fremantle midfielder Shai Bolton was awarded the Norm Smith Medal as best afield.
Brisbane midfielder Will Ashcroft (31 disposals, nine clearances) and co-captains Harris Andrews and Josh Dunkley were fantastic in the comeback win, along with forward Charlie Cameron (three goals) and veteran Dayne Zorko.
Dunkley told Channel Seven that they were ready for Wharfie Time and used it as fuel for their comeback.
"We talked about Wharfie Time and making that our energy and I felt like when I looked around at centre bounce and Wharfie Time came on, we all looked at each other and we connected and we grew a leg, and then got it done," he said.
Dockers midfielders Caleb Serong (13 clearances, 24 disposals) and Hayden Young (two goals, 22 disposals) were excellent, while Voss kicked three goals.
Brisbane champion and former Docker Lachie Neale, who contentiously had his one-game striking ban overturned at the AFL appeals board on Thursday, was heavily booed by the Fremantle fans throughout.
Heavy rain on Saturday morning meant covers were on the ground before the pre-game entertainment, headlined by Kylie Minogue.Â
There was some rain during the match, with conditions cold and overcast throughout.
Fremantle will be left to rue botched chances as they narrowly missed their first premiership since entering the AFL in 1995.
The Dockers kicked a wasteful 6.10 in the second half, and key forward Josh Treacy will have nightmares about a shot he missed from the goal square, midway through the last quarter.
For the second straight year, scores were level at the main break of the grand final after a scrappy and frenetic first half that featured nine lead changes.
As the Dockers opened the third term with a wave of attacks, Pearce was hunting the ball on the members' wing when he suddenly dropped to the ground, as if shot.
He was immediately helped to the interchange bench by two trainers and had ice put on his right lower leg.
Despite losing their captain and defensive general, Fremantle did not break stride. When livewire goalsneak Isaac Dudley snapped a brilliant goal at 12 minutes, the Dockers led by 15 points.
Then, a week after his improbable goal against Sydney in Fremantle's comeback preliminary final win, Young kicked another one from the boundary to give the Dockers a 10-point break at three-quarter time.
There was controversy at the end of the first term - an incident that was magnified by the tight final margin.
Treacy took a mark and thought he had a set shot from inside 50m, but the umpire said the pass to Treacy was not 15m - it clearly was - and he was tackled for a ball-up.
18°C