The Blues led for the entire third quarter and took a 10-point advantage into the last change before the Magpies kicked eight of the last 11 goals to win 17.15 (117) to 15.10 (100).
Collingwood's pressure went to another level in the fourth quarter and small forward Jamie Elliot stood up to kick two clutch goals, finishing a brilliant performance with five.
The final margin didn't reflect how close and hard-fought the final stages were, with late goals to Steele Sidebottom and then Scott Pendlebury, in his 150th game, stretching the gap.
In a finals-like atmosphere with a crowd of 84,247, Elliot and rookie Sam Dwyer stood up to play big games with the Magpies handicapped by an early injury to ruckman Darren Jolly, who cracked a rib.
Elliot pushed up the ground and took 10 marks, finding space in a game where there was little, and his cool set shot from 40m on an angle proved crucial with three minutes remaining.
Dwyer, meanwhile, finished with 23 possessions (14 contested) and a goal in just his second game.
Heath Shaw was also involved in a number of key plays – both in defence and forward – finishing with an equal game-high 26 disposals and a goal.
Collingwood coach Nathan Buckley said he enjoyed the nature of the victory against an opponent that had given the Pies trouble in recent times, rather than what it meant to beat a Malthouse-coached side.
"The win itself was excellent. I said to the players, 'I enjoyed that win'," Buckley said.
"After losing both games to Carlton last year, we've identified the first three weeks as opportunities for us against sides we weren't able to beat in 2012.
"To the players' credit, they've been able to execute the plan.
"That is satisfying but it lasts a moment in time and then we fast forward and look at the Hawks as quickly as we can."
The margin on Sunday hovered between one and two goals much of the thrilling final term, with Jeff Garlett, Lachie Henderson and Kane Lucas all kicking goals to keep Carlton in the contest.
The Blues were well served by their small forwards, with Garlett, Chris Yarran and Andrew Walker kicking three goals apiece.
The hype around Sunday's clash centered around Malthouse coaching against his former club and Buckley, his successor at Collingwood, but the on-field drama surpassed the pre-game storylines.
Asked if he was glad to have the game and the build-up out of the way, Malthouse said: "That's life. I've been in big games before, that's the way it is."
Malthouse chose to deploy run-with specialist Andrew Carrazzo on Pendlebury and the star midfielder was well held early before playing a key role in the last term.
Meanwhile, Brownlow medallists Chris Judd and Dane Swan ran head-to-head from the opening bounce in a match-up that favoured Carlton. Sidebottom would eventually go to Judd.
The Magpies relied on Jarryd Blair and Sidebottom to do their midfield grunt work for three quarters, but weight of numbers told in a fourth quarter that saw Collingwood win the clearances (11-7).
They ran harder and smarter for much of the second half, winning the uncontested possessions 114-71 after the main break.
"We played probably one of the best sides in the competition … they might even be No.1," Malthouse said post-match.
"They were better when it counted most. They were smarter with the footy and they just worked a bit harder.
"If that's the plus, the minus is we weren't smart with the football and we didn't work hard enough."
Collingwood effectively lost Jolly at the four-minute mark of the first quarter and he was subbed out in the opening minutes of the second term after attempting to return.
Quinten Lynch stood up and led the ruck against Matthew Kreuzer, battling hard to finish with 19 hit-outs and six clearances.
Captain Marc Murphy was superb for the Blues, winning 17 of his 26 possessions in contests, while Judd faded after a strong first half, with Sidebottom's role influential.
Sam Rowe made his debut for Carlton, less than 12 months after being diagnosed with testicular cancer, and contributed with a goal and eight hit-outs.
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Collingwood: Elliot, Shaw, Dwyer, O'Brien, Clarke, Lynch, Pendlebury
Carlton: Murphy, Kreuzer, Yarran, Garlett, Judd, Gibbs