Speaking after the loss Lyon heaped praise on the Bombers, who have won through to the NAB Cup grand final where they will take on the winners of Collingwood and West Coast.
"It wasn't ideal. I'm glad it's NAB Cup. I'm glad we've got a couple of weeks to fix it up. I thought Essendon were terrific," Lyon said.
"They played like a hungry team and they really coordinated and harnessed their talent. I just think they are going to go a long way and challenge. It was like a top-four performance really."
St Kilda defender Sam Fisher looked to be in serious trouble when he came off the ground with a facial injury early in the first term and went straight to the rooms.
But Lyon said the early assessment would see Fisher right for the round one clash with Geelong.
"He copped a whack in the face. I did speak to the doctor and he said it would be a week maximum," he said,
"I'd be incredibly flat if he wasn't going to be there for round one, but he will be there so we're pretty happy."
While Lyon was full of praise for the Bombers, he admitted to some minor concerns at the performance of his own side, which relied on rookie Daniel Archer to shoulder the ruck load in the absence of Michael Gardiner, Ben McEvoy, Justin Koschitzke and Rhys Stanley.
"We've really got some strong wake-up calls. I think it highlights that at this level how quickly you can get exposed. I'm not happy about it but I'm sure we can turn it around," Lyon said.
"It highlights the importance of ruckmen as well, I thought he kids battled on manfully but we got cleaned at stoppages and our skill level was really poor and their pressure was really good. It was a combination."
