Umpire Matt Stevic paid a free kick for in the back against Cameron Mooney just before Cameron Ling gathered a loose ball and kick what would have been the winning goal for the Cats.
Mooney was seen to vent his frustration at the umpires after the decision, which is sure to be discussed heavily in the coming days and
But Lyon said the decision had merit in his eyes.
“You see it go through but I thought as the play unfolded, I thought there was a free kick there. No doubt about that,” Lyon said after the game.
“But they don’t [always] get paid. I wasn’t sure whether it had been paid or not.
"It’s a tough night for everybody - umpires, both teams. You always need a little bit of luck after you worked your hardest. I thought we worked incredibly hard and I think in the end, from my side of things, we did a lot right to be able to say we were deserved victors.”
The win has given St Kilda a preliminary final berth in what is seen to be the weaker half of the finals draw - not that Lyon was in any mood to discuss what faced the Saints in the coming weeks.
“It’s interesting you talk about grand finals,” he said to one reporter.
“All I know is my next game is a prelim final and we are going to have an elite opponent. I haven’t got that luxury. I look one week at a time and we prepare for what is going to be round 24.”
The Saints looked to have the game almost in the bag in the third quarter when they got away to a 33-point lead as heavy rain started to fall.
But Lyon said he never had a sense that the game was won, and admitted his mind drifted back to last year’s grand final when poor kicking for goal saw the Saints go down to the Cats.
“I never relax. It’s folly. Thirty-three points, as you saw, can be whittled away in five or 10 minutes of footy. I was conscious that we weren’t taking the opportunities and missing some of those snaps were reminiscent of ’09 I suppose,” he said.
“And then the counter attack made me really nervous. I think it fuelled their belief. If we had have taken our opportunities and shut the game and the 30 becomes 50, I think the fuelling of their belief dissipates and it’s very hard from there.
"Once they scored easily it fuelled their belief and they came again. That’s what great sides do. It’s undeniable what they’ve been and what they are."
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