Winless in his first three Origin deciders, under-fire halfback Cleary helped the Blues to a surprise 18-0 lead by scoring two first-half tries and stripping the ball ahead of their third.
Game-ending head injuries to veteran fullback James Tedesco and first-gamer Jack Bostock weakened the Blues, who were troubled by the injection of Maroons livewire Reece Walsh in the second half.
Chasing points, the Maroons had a try chalked off that would have put them six points behind in the final 15 minutes, with the bunker ruling Max Plath had been offside chasing Sam Walker's kick.
Wally Lewis Medallist Cleary then nailed a penalty goal that made it a three-score game, all but putting the result beyond doubt.
"It's unbelievable, this group of players, they're just freaks," Cleary told the Nine Network.
"I love playing alongside them. The belief - we were all written off and came together as a group."
It marked only the Blues' fourth victory in a decider at Suncorp Stadium from 14 attempts, and their first time winning consecutive deciders at the venue following their 2024 triumph.
The victory came after the Blues were written off by all and sundry, having conceded 36 second-half points in a demoralising 20-point game-two loss.
With last year's series loss fresh in memory, coach Laurie Daley faced heavy scrutiny ahead of the decider.
"It feels pretty special... We know that performance was there, but we just haven't seen it, so it was all about proving ourselves right rather than proving anyone else wrong," Daley said.
No player had been under more pressure to deliver in Brisbane than Cleary, for so long criticised for his track record in big Origin moments.
The four-time premiership winner wasted little time silencing his doubters on Wednesday night.
After an error-prone start from the Maroons, Cleary had the Blues' first try stepping inside Kurt Capewell at close range and gliding over.
Blues second-rower Liam Martin, back from a knee injury, burst through Cameron Munster and found Stephen Crichton, who flicked to Mark Nawaqanitawase ahead of Cleary's second try.
In the Maroons' next set, Cleary stripped the ball from Selwyn Cobbo to put the Blues into position for another four-pointer through Cameron Murray.
The Blues lost Tedesco in the final minute before half-time when the former captain clashed heads with Maroons second-rower Briton Nikora.
Tolu Koula came on at fullback, before the Blues were forced into another backline reshuffle when winger Bostock fell awkwardly contesting a kick.
Walsh and Kalyn Ponga combined to give the Maroons a sniff, the pair helping Cobbo to a try and cutting the deficit to 10.
But just as the Maroons were on the attack again, Jojo Fifita fumbled Walsh's kick into the arms of Bradman Best, who ran 100 metres to score the Blues' fourth.
After Fifita atoned on the right, the Maroons thought they had a fourth try when Koula allowed a Walker kick to bounce up for Rob Toia.
But the offside penalty against Plath thwarted the Maroons and the Blues held on, with Hudson Young crossing late.
"I think we probably saved some of our worst for last," said Queensland hooker Harry Grant.
"This game tonight was probably not our best one. We probably would have liked to have back."
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