Thomas left the ground before half-time in his comeback game for Collingwood in the VFL on Saturday against Sandringham.
He had scans on Sunday to determine the extent of the injury.
He will consider a range of options ranging from further rest to more surgery to repair the damaged ligament.
Doc Larkins' verdict on Daisy Thomas
The premiership midfielder has not played senior football since round seven after undergoing his second ankle operation in the past 12 months in May.
The first operation on his ankle took place in November, and the start of Thomas's season was delayed until round 3 against Hawthorn.
He played just five games in 2013 before the decision was made to operate on his ankle.
Thomas is disappointed with the development after working very hard to make a comeback in an attempt to play finals.
With Thomas' season over, Collingwood's interim director of football Rodney Eade said the focus was to ensure he made a full and lasting recovery.
"He is going to see several specialists over the next week or so and in terms of what, if any, impact there will be on his pre-season we will have to wait and see," Eade said.
"A clearer picture of what the options are will emerge once he has been examined."
Out of contract at the end of the season, Thomas had delayed contract talks until he was back playing.
He is expected to have a better understanding of what course of recovery he will take early next week.
Collingwood has also lost senior players Jamie Elliott and Ben Sinclair to injury on the eve of the finals.
Elliott suffered from hamstring tightness late in the game against Hawthorn on Friday night while Sinclair hurt his shoulder.
Both have been ruled out of Friday night's game at the MCG against West Coast but are expected to return for round 23 against North Melbourne.
