Wales' Grand Slam captain in 2005, Owen has been out of the Wales squad since Wearren Gatland took over as coach and had hoped to use his move from the Dragons to Saracens as a launch pad for a Test recall.
Gatland and his coaching team had been monitoring his progress in the Guinness Premiership, but now the 28-year-old's season has been brought to a premature close through knee surgery.
The 41 times capped back row man picked up the problem against Gloucester and has now been forced to undergo knee surgery.
"Michael picked up a knee injury against Gloucester and it proved to be more serious that we first thought," said Saracens coach Eddie Jones.
"He's had to have reconstructive surgery and that will rule him out for the rest of the season. It's frustrating news as he has been playing very well for us this year."