Owen suffered the injury during the Carling Cup final victory over Aston Villa on Sunday.
“It’s a bad blow – he’s out for the season,” Ferguson said. “Unfortunately it’s more serious than we thought. He will be operated on on Monday morning.
“It’s a terrible blow for the lad and is disappointing news for us too.
“He has never missed a training session all season.
“I think the heavy pitch at Wembley on Sunday made some contribution to it but really it is just bad luck.”