A controversial umpiring decision denied Geelong captain Cameron Ling what would have been a match-winning goal as St Kilda survived a four-point AFL qualifying final thriller at the MCG on Friday night.

The Saints led by as much as 33 points in the third term but had to hold on desperately to win 12.11 (83) to 11.13 (79) as the Cats surged home in driving rain.

After kicking five of the last six goals of the third quarter, Geelong outscored the Saints 1.7 to 1.0 in a final term, in which the ball spent the majority of the time in their attack.

The Saints led from late in the first quarter but the Cats came incredibly close to snatching the lead with 61 seconds left on the clock.

Ling pounced on the ball at half-forward after a Cameron Mooney tackle on James Gwilt caused it to spill.

The Cats captain's shot bounced over the goal line as a push-in-the-back free kick was being paid against Mooney for landing on Gwilt as he followed through with the tackle.

The win gave St Kilda their first AFL finals victory over Geelong, their grand final conquerors of last year, earning them a weekend off and a preliminary final berth.

The Cats will have to return to the MCG next Friday night to face the winner of Saturday's Subiaco clash between Fremantle and Hawthorn, after losing on the opening weekend of the finals for the first time in four seasons.

The Saints had control for most of the first half, key forwards Nick Riewoldt and Justin Koschitzke on fire in the first term, with 10 marks and 3.2 between them to set up a nine-point lead.

Small forward Stephen Milne did the damage in the second term, with three goals in six minutes, as the Saints shot 20 points clear at the main break.

The Saints looked set to stream away with the match when they added two more goals in the first five minutes of the third term, to Clint Jones and Leigh Montagna, to stretch the gap to 33.

But, with heavy rain starting to fall during the halftime break, the game completely changed complexion.

Ling moved onto Goddard, who was best afield in the first half with 20 touches, keeping him to just six disposals in the second half.

Joel Corey replaced Josh Hunt on Milne, stopping the Saints' goalsneak's influence and providing plenty himself.

Midfielder Joel Selwood recovered from a horror first half, in which he had just four touches, to pick up 15 in the second, while fullback Matthew Scarlett prevented Koschitzke from gaining a disposal in the final three quarters.

With midfielders Gary Ablett, Jimmy Bartel and Paul Chapman continuing their solid first-half work, the Cats dominated in general play, but a series of missed shots and some desperate Saints defensive work just kept them at bay.

Geelong coach Mark Thompson was clearly upset as he strode onto the ground after the final siren, but avoided risking a fine by publicly criticising the umpires, particularly Matt Stevic, who made the pivotal decision.

"You write whatever you want to write, and write the truth about that last incident, that's all I'll say," he told reporters.

"I don't want to risk any fines, I'm not going to say anything about the umpires. I'm sorry, I can't."

But he did not spare his own players, saying while he was happy with the way they finished the game, the first half was unsatisfactory.

"I said `the next game we play, we better make sure that if you're not prepared to play well from the start then don't turn up and play for this club', and I meant it," Thompson said.

"You see the boys jumping in late in the game when they were a chance to win and be really desperate, we want people to be desperate at the start of the match."

St Kilda coach Ross Lyon said his side deserved the victory, although he admitted they were fortunate in the end.

"I thought as the play unfolded, I thought there was a free kick there, no doubt about that, but they don't (often) get paid," Lyon said.

"I wasn't sure if it had been paid or not, it was a tough night for everybody, umpires and both teams, and you always need a little bit of luck after you've worked your hardest and I thought we worked incredibly hard.

"I think in the end from my side of things we did a lot right to be able to say we were deserved victors."

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