Magennis suffered ligament damage but the extent of the problem will not be known until after he has had a scan.
"It's not looking great," said Goodwin. "He’s our captain on the night and he does a fantastic job for us.
"He’s going for a scan tomorrow morning but, at this moment in time, it’s not looking good.
"He’s definitely done ligaments, it’s just a question fo whether it’s medial or cruciate. But it’s six to eight weeks, anyway.
"To lose a player as influential as Kyle, with such a serious injury, is disappointing for him - and he's going to be difficult to replace."