Small forward Tyson Stengle was about to have a shot to put the Cats 33 points ahead on Friday night, before the ball was taken down the other end of the MCG.
Geelong's Mark O'Connor was controversially penalised for shoving Rayner in the back in the Lions' goal-square.
In a rush of blood, Cats defender Zach Guthrie ran in to remonstrate with Rayner after the Brisbane premiership winner had reduced the margin to 21 points.
Rayner fell to the ground, leading the umpire to pay another free kick immediately.
Instead of being more than five goals ahead, Geelong led by just 15 points at the main break to give the lacklustre Lions some belief.
"It pissed us off, to be honest - they had three goals like that (from free kicks) in that (second) quarter, and it revved us up," Geelong star Max Holmes told AAP after the Cats' eventual 16.16 (112) to 11.8 (74) triumph.
"So it might have helped us a bit in the end.
"But there's nothing you can do about that. It's uncontrollable.
"So we just put our heads down, we still had the lead when they had those goals.
"It was one of those ones where we just knew we were dominating them the whole day."
Geelong coach Chris Scott was proud of how his players didn't become distracted by the situation.
"For the most part, that was handled pretty well on our part," Scott said.
"I don't think I've heard our crowd as engaged as they were, and maybe that was something that sparked them even more.
"It was so far away you couldn't see it in the behind the goals vision.
"Fortunately, one of my colleagues in the box said you don't want to see it on the broadcast vision, so I didn't see it until post-game."
Rayner leant into being the villain of the fired-up Geelong crowd,
The star of last year's preliminary final win against the Cats when he booted the matchwinner, Rayner was barely sighted before being moved to full-forward.
The 25-year-old booted the Lions' first goal of the third term, then celebrated in front of Geelong's cheer squad.
Rayner was booed every time he went near the ball for the rest of the game.
"It was a hostile crowd, there was a lot of Geelong supporters here tonight," Lions coach Chris Fagan said.
"That would have been Cam's way of just trying to bring a little bit of energy for the team.
"So no issue with that."
But the controversy mattered little as Geelong cantered to a comfortable 38-point win, gaining some revenge for their season being ended by the Lions last year.
The Cats booked a spot in a 14th preliminary final since 2007, while Brisbane will be forced to go the long way if they want to back up last year's premiership.
They will head back to the Gabba for a semi-final against the winner of Saturday night's elimination final between Fremantle and Gold Coast.
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