McStay kicked vital two goals in the Magpies' thrilling one-point preliminary final win -Â 8.10 (58) to 8.9 (57) - over GWS on Friday night before hurting his right knee during the third quarter.
He tested the joint but was ruled out at three-quarter time with the game still hanging in the balance.
McStay cut a despondent figure amid otherwise jubilant scenes in the Collingwood change rooms after the match.
"He's going to get scans. I'm not great with the terminology, I'm not sure if it's an MCL," Magpies coach Craig McRae said.
"I'm not sure yet, so we'll get scans. I don't want to put a definite decision on it but I think he might be unlucky to miss out. We'll wait and see.
"At the moment, until you really know, you put your arms around him and show love and support as best you can.
"That'll play out pretty quickly, I would've thought."
McStay moved from Brisbane as a free agent at the end of last year and missed three months of his first season at Collingwood with an injured finger, which was operated on and then became infected.
He returned in round 18 and has kicked multiple goals in eight of the Magpies' last nine matches, taking his tally to 20 in 14 appearances in black-and-white.
McStay kicked Collingwood's first goal in the preliminary final and caused problems for the Giants' defence in a low-scoring contest.
"He had moments. Early he was significant, jumping and marking the ball," McRae said.
"You could see why he's important to us - we need someone who can mark the ball forward of centre.
"If he doesn't quite get up, he'll be missed."
Collingwood vice-captain Taylor Adams is also in significant doubt for the season decider after sitting out the preliminary final with a hamstring injury.
"That's going to be a watch the clock," McRae said.
"I think every second is going to be needed. We'll push it to the line and see how we go."
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