Owen will undergo surgery on the hamstring Injury which forced him out of the Carling Cup final at Wembley.
It means the end of Owen's fading hopes of gatecrashing Fabio Capello's World Cup squad for South Africa.
United boss Sir Alex Ferguson said: "Michael is out for the season.
"He will have an operation on Monday morning. It's a terrible blow for the lad and disappointing for us too.
"He hasn't missed a training session all season. But I think the heavy pitch at Wembley didn't help, as well as an element of bad luck."