The 22-year-old came off the bench at half-time in the semi-final first leg defeat to Swindon Town.
But he lasted until just the 88th minute after suffering a hamstring strain.
Asked if Scougall would miss Monday’s return leg, manager Nigel Clough said: “Scouggs is out, yes.
“It is his hamstring. That’s Stefan’s season gone now. Even if we were still in the season itself, he’d be looking at three to four weeks.
“It’s all about, for him, getting ready for pre-season.”
John Brayford was another Blade to be forced out of the loss to the Robins but he may recover from a knee injury.
Clough, meanwhile, is hoping to use what he sees as a major injustice in terms of poor decisions by referee Darren Bond as a galvanising tool in Monday’s second leg.
He added: “The feeling is still there. To play like that and come off with a defeat was very hard to take.
“At the moment, it’s still fresh but we’ll speak to the players and get them to use it. We are still in the tie.”