A contentious holding-the-ball decision against Hawks defender Jarman Impey gave Hugh McCluggage a free kick and he kicked the match-deciding goal with 18 seconds left.
Brisbane then won the centre bounce and Kai Lohmann kicked another goal on the siren to seal a nine-point win, 20.11 (131) to 19.8 (122), in front of 97,835 fans at the MCG on Saturday.
"Has there ever been a more exciting game of AFL football than that one?" Lions coach Chris Fagan said.
"If I was a spectator, I'd just be rapt by that.
"Hawthorn are unlucky, no team deserved to lose tonight.
"We're just lucky enough that we were in front when the siren went and we get to fight another day."
The Lions are aiming to become the third team this century - Brisbane in 2001-03 and Hawthorn in 2013-15 - to pull off a three-peat when they meet Fremantle in a final for the first time next Saturday.
But after losing one of the AFL's greatest ever games, Hawthorn will seethe over the Impey decision, which prompted co-captain James Sicily and defender Tom Barrass to blast the umpires.
"I don't think anyone's going to be sleeping that well tonight after how that last goal went down," Barrass told the Seven Network.
Hawks fans were in uproar after the final siren and a bottle was thrown at the umpires as they left the field, after their team had rallied from 28 points behind during the last quarter.
Hawks coach Sam Mitchell took more issue with preceding calls - a high free kick paid to Dayne Zorko, and another where forward Mitch Lewis was penalised for showing "insufficient intent" to keep the ball in play.
Asked if the Impey call was a free kick, Mitchell said: "I haven't rewatched it. Maybe.
"There were a few. It's probably not the one I was focused on - a couple that led up to it and some key moments in the game.
"I'm sure the umpires will assess how they performed in that game, in key moments - the Mitch Lewis out-of-bounds one and the Zorko free kick, but not for me to say."
Fagan believed the Impey free kick was there.
"I didn't necessarily have the greatest of views, but it didn't look like Impey was actually trying to get the ball out," Fagan said.
"I think that's what caused the umpire to pay the free kick."
There were nine lead changes - four alone late in the final term.
Key forward Lewis took a soaring mark and kicked a goal to put Hawthorn back in front late.
Barrass and Sicily then took two massive defensive marks, but the Lions went forward again and the crucial free was paid.
"If you want to strive for great things, you will open yourself up for all sorts of emotion, the greatest of joy, and the deepest of pain," Mitchell said.
"That was a game for the ages. I'm sure I'll appreciate it at some point, but right now I would rather be anywhere but here."
Hawthorn's Nick Watson, dubbed "The Wizard", was best afield with a magical six goals, and was instrumental in their brave last-quarter charge.
Trailing by 22 points in the second term and 16 points in the third, Brisbane went on a scoring rampage that appeared to have decided the game, before Hawthorn's outstanding rally.
McCluggage's ice-cold match-winner capped a 23-disposal, three-goal showing.
Will Ashcroft (28 disposals, eight clearances) and Lachie Neale (26, nine clearances) were strong, and co-captain Harris Andrews cut off multiple Hawthorn attacks.
Fagan said Neale only suffered a hit to the chest, not a head knock, after he was collected by Jai Newcombe in the first minute of the game.
Lohmann (five goals) turned the game with a three-goal third quarter.
Hawks Jack Gunston (five goals) and Lewis (four goals) hit the scoreboard in Hawthorn's highest losing score since 2005, while Josh Ward (11 clearances, 25 disposals) was huge.
