The Magpies trailed all game until the 29-minute mark of the final quarter, when Beau McCreery snapped a brilliant goal on the run.
Collingwood hung on to win 11.13 (79) to 11.12 (78) in a result that keeps their finals hopes alive ahead of their final home-and-away game against Melbourne next Friday night.
Oft-maligned recruit Lachie Schultz stepped up late with two crucial goals, before McCreery slotted the match-winner.
The Lions exploded out of the blocks with the first four goals of the match to lead by as much as 31 points late in the first quarter.
But Collingwood superstar Nick Daicos produced one of the all-time great quarters to boot two goals and gather 13 possessions in the second term to lift the Magpies back in the contest.
Collingwood's Nick Daicos kicked two goals and had 25 disposals against the Lions. (Rob Prezioso/AAP PHOTOS)
The Magpies can still finish in the top eight should they beat Melbourne on Friday night, and other results fall their way on Sunday and next weekend.
Brisbane were made to pay for blowing a number of gettable chances during the third quarter through Cam Rayner, Zac Bailey and Will Ashcroft to leave Collingwood just 14 points behind at the final break.
The Lions appeared home when Charlie Cameron's clever snap put them 17 points in front at the 20-minute mark of the final quarter.
Brisbane spearhead Joe Daniher then had the opportunity to bury the Magpies, but he sprayed a set shot and his chance at his fifth goal of the match to leave the door ajar for a trademark Collingwood comeback.
The Magpies took that opportunity and surged home in remarkable fashion in front of 61,218 fans.
After winning six straight games against Collingwood, the Lions have had three painful losses in a row against the Magpies, including last year's grand final by four points.
The Lions' hopes of securing a top-four finish appear shot, with this result coming on the back of a defeat to GWS at the Gabba last Saturday.
Lions midfielder Jarrod Berry was subbed out in the second quarter with hamstring tightness, replaced by wingman Harry Sharp.
Brisbane will complete their home-and-away campaign at the Gabba next Saturday night when they host Essendon.
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