The French midfielder, outstanding on the night, went down from a reckless tackle and was taken off the filed in obvious pain.
It is believed that the former Southampton star has damaged his knee although the player will undergo a scan in the next few days to find out the extent of the damage.
If Folly is out for a long time which looks to be the case, it will be another hammer blow to Paul Sturrock who is already without key players Richard Wood, Deon Burton, Steve Adams, Barry Corr, Drew Talbot, Marcus Tudgay and Peter Gilbert for the foreseeable future as well as the suspended Lee Bullen.
The Owls had at least two clear penalties ruled out and in a dominating performance, Wednesday's failure to create any major chances in front of goal was their undoing.
Sturrock said afterwards: "I'm gutted for the players. I'm proud of their attitude and the spirit was there to see. We had 30 crosses and 20 shots in the game but didn't hit the target often enough with headers and half-chances."