Down 24-8 with 18 minutes to play, Cleary set up two tries and scored one of his own in the dying minutes to give the Panthers the lead and earn himself a second Clive Churchill Medal.
The most crucial of those came with three minutes left when Cleary darted back through the middle of the field to score and then convert take a two-point match-winning lead.
Penrith then held on for the final minutes, with Scott Sorensen intercepting a Reece Walsh offload to end Brisbane's hopes of victory.
The win overtakes Melbourne's comeback from 14 points down against St George Illawarra in 1999 as the biggest-ever in a decider.
The victory also stakes Penrith's claim as one of the all-time great rugby league sides, becoming the first team since Parramatta in 1983 to win three straight titles.
But it hasn't been completed in the NRL era or under a salary cap.
Making Cleary's effort even more remarkable was that he did it without five-eighth Jarome Luai, who succumbed to a shoulder injury with 28 minutes to play.
Penrith looked shot early in the second half when Ezra Mam scored three tries in the space of 10 minutes to take Brisbane from 8-6 down to a 24-8 lead.
All three tries came from a distance, with Mam stepping past Lindsay Smith and Izack Tago for his first and Isaah Yeo and Cleary for his next.
Walsh then inserted himself into the game, stepping past Cleary, fending off Tago and putting Mam over for his hat-trick.
But after his two defensive lapses, Cleary made up for it as he masterminded a Penrith fightback.
With 18 minutes to play, Cleary stepped through the Broncos' line and put Moses Leota over, reducing the margin to 10.
From the next set he produced a pinpoint perfect 40-20, before sending Stephen Crichton over moments later following a Pat Carrigan error.
Then, just as Brisbane looked set to hold on, Cleary stepped through a broken defensive line to give the Panthers their fifth title and by far their most miraculous.
Penrith had earlier dominated the first half, but only had an 8-6 half-time lead to show for it when Thomas Flegler crashed over for Brisbane right on half time.
Despite their charge, the loss means the Broncos' premiership drought will extend into a least an 18th season.
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