United blamed the poor state of the Wembley pitch for the hamstring injury Owen picked up during the Carling Cup final last week.
The blow rules out any small chance Owen had of going to the World Cup.
Game over: Michael Owen (right) winces as he chases the ball at Wembley
'It's a bad blow - he's out for the season,' said Ferguson. '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.'
Seventh heaven: Michael Owen (far right) scores against Villa at Wembley
The 30-year-old, who has been struck down by a number of long-term injuries in a tumultuous career, has failed to secure first-team football since going to Old Trafford on a free transfer in the summer.
Owen, who left Newcastle at the end of last season, signed a two-year deal with United worth £20,000 a week, plus more based on performances.
The former Liverpool star scored United's first after being handed a shock start in the Carling Cup final on Sunday, but was forced off in the first half after pulling up with the hamstring injury. He later joined the on-pitch celebrations after United secured a 3-1 win.
Dejection: Owen is replaced by Rooney at Wembley
England manager Fabio Capello insisted this week that Owen still had achance of going to South Africa this summer, but the striker admittedhimself that he was a 'long shot' after playing no part in theItalian's sides.
Now, after learning the extent of his injury, Owen said: 'Unfortunately the specialist says I will miss the end of the season.
'I have loved every minute of my first campaign with Manchester United and have already enjoyed some memorable moments.
'I am determined to come back at the start of next season in peak condition.'
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