Magennis, who had only returned from a four-game ban in the convincing midweek win over Preston North End, is facing between six and eight weeks out after tearing his hamstring in training ahead of facing the Tykes.
Stewart, meanwhile, is set for an even longer spell on the sideline after it was confirmed that the midfielder had broken a bone in his foot.
“Josh is going to be out for about six to eight weeks with a grade two hamstring tear,” said McCann after the loss at Oakwell. “Six weeks if we’re lucky.
“He did it in training yesterday, just a back heel. It was innocuous really – he just tried to keep the ball in play with nobody near him. That’s disappointing.
“Kevin Stewart will also probably not be back until the back end of February. He’s cracked a bone in his fifth metatarsal so he’s going to have to get that pinned. They’re big losses but it now provides opportunities for others.”