Dempster, 24, has played 19 games for the Saints since crossing from the Swans in a package deal including Adam Schneider at the end of last season. He sustained the injury that will likely require reconstructive surgery in a tussle with Bomber Mark McVeigh in a marking contest in the opening minutes of the match.
"Sean Dempster, who I might say has been fantastic for us – I reckon Schneider and Dempster have been fantastic for us, they've both delivered for the majority of the year – but unfortunately he did his ACL, it looks like, in the first minute of the game," Lyon said.
The seemingly innocuous incident left Dempster prone on the turf for a minute before he left the ground under his own steam, but his entire 2009 season is now at risk as a result.
"It's a loss for us, we feel for Sean – I can't imagine what he's feeling at the moment – but he'll be assessed fully in the ensuing days," Lyon continued.
"We've got great surgeons and great rehabbers, and Brendon Goddard has shown just what can be done coming off a reco, so he'll come back and play for St Kilda again."
Dempster, who has a career tally of 73 games, was recruited by the Swans under the father-son rule at the 2002 NAB AFL Draft and played in the 2005 premiership side before being traded for pick 26 last year.