Fremantle led by 17 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 join Hawthorn (2013-15) and the legendary Brisbane team of 2001-03 to win three premierships in a row this century.
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, before Brisbane reeled them in, delivering coach Chris Fagan a third premiership amid heavy speculation it was his final game at the helm.
Brisbane midfielder Will Ashcroft (31 disposals, nine clearances) and co-captains Harris Andrews and Josh Dunkley were fantastic, along with forward Charlie Cameron (three goals) and veteran Dayne Zorko.
Dockers midfielders Caleb Serong (13 clearances, 22 disposals) and Hayden Young (two goals, 24 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, but the weather cleared up ahead of the main event
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