Owen suffered a hamstring injury in the Carling Cup final win over Aston Villa on Sunday.
“He’s not had a lot of football and the pitch probably wasn’t the best for him,” said Ferguson.
“You pick the team before you know the pitch conditions, and Michael isn’t suited to a heavy pitch like that. We paid the penalty for it.
“That aside, I thought he was one of our best performers in the first half. He did really well for us and scored a goal to get us back in the game.
“He’s good at picking up crumbs. He’s as good as anybody at that.
“He and Rafael will go for scans tomorrow, I think Michael will be out for a few weeks.”
Rafael da Silva was forced off through injury in the second half.