Lions midfielder Ryan Lester had the chance to snatch what would have been a remarkable victory, only to mistime his flying snap in the final second, allowing Paul Chapman to rush the ball through for a point.
The nail-biting 15.22 (112) to 17.9 (111) victory ensured Geelong would finish the home and away season in second spot, booking a home qualifying final next Saturday against Fremantle.
The only way Brisbane could have remained in finals contention was if they had become just the second team in nearly six years to beat the Cats at their regular home ground.
The visitors led by as much as 10 points during the third term, but Geelong were able to steady with the last three goals of the quarter - including two similar crowd-pleasing snaps from Travis Varcoe and Allen Christensen.
The Cats extended that advantage to 26 points early in the final term, only for Brisbane to come home much the stronger.
Brisbane kicked three of the last four goals of the match - two of them to Jordan Lisle - but it wasn't quite enough.
McGrath - the hero of Brisbane's remarkable come-from-behind win against the Cats at the Gabba earlier in the year - was the dominant forward on the ground with six goals.
Geelong shared the load, with 12 individual goalkickers.
Brisbane kicked the opening goal of the game through McGrath, the only member of Saturday's lineup who featured in any of their triple premierships teams early last decade.
Geelong did not take long to steady, kicking four of the next six majors to lead by 14 at quarter-time.
When James Kelly kicked the opening goal of the second quarter, it looked like the Cats were on the way to yet another routine victory at a ground where they had won 42 of their previous 43 matches dating back to early 2008.
But the Lions regrouped to kick seven of the next seven goals - including five in succession - to take an improbable six-point lead into the long break.
The momentum continued to swing throughout a thrilling second half.
Having come up just short on Saturday, Brisbane will now turn their attention to finding a new coach to replace Michael Voss.
GEELONG 5.5 7.11 12.20 15.22 (112)
BRISBANE 3.3 9.5 11.6 17.9 (111)
Goals: Geelong - Caddy, Chapman, Varcoe 2; Christensen, Taylor, Bartel, Kelly, Podsiadly, Selwood, Duncan, Johnson, Hawkins. Brisbane - McGrath 6; Lisle 3; Zorko, Green, Lester 2; Golby, Bewick.
Best: Geelong - Bartel, Johnson, Stokes, Duncan, Caddy, Chapman, Selwood. Brisbane - McGrath, Golby, Rockliff, Redden, Rich, Yeo.
Umpires: Stephen McBurney, Chris Kamolins, Heath Ryan.
Official Crowd: 27,483 at Simonds Stadium.