Thomas lasted less than a half in his VFL comeback on Saturday, after three months out following ankle surgery, before a knock to the ankle forced him out.
Even before the setback, Collingwood coach Nathan Buckley had forecast the 26-year-old faced a challenge to work his way back into the senior side for the finals.
Thomas was forced out of the game, for Collingwood's VFL side against Sandringham, partway through the second quarter.
"Dale received a knock to his ankle in a contest during the second quarter," VFL coach Dale Tapping told Collingwood's website.
"We withdrew him from the rest of the match for precautionary reasons and I'm sure he will be assessed on Monday."
Thomas had four possessions before the injury.
The Magpies star is out of contract at the end of the season and yet to announce whether he will remain with Collingwood next year.