The England midfielder has been struggling with a serious tendinitis problem in recent seasons and has undergone operations on both knees.
Hargreaves has been included in United’s squad for the Champions League ahead of Zoran Tosic and Ritchie De Laet.
Ferguson said: “The difficulty was around what we should do with Owen Hargreaves, whether or not to put him or Zoran in the squad.
“It was Owen or Zoran or Ritchie de Laet. It was a dilemma. But we came down on the side of Hargreaves because having taken the medical advice we think he will be available for the last three Champions League games.
“We came down on the side of Hargreaves because, having taken the medical advice, we think he’ll be available for the last three Champions League group stage games.
“He’s a versatile player who can perform in so many positions, so he could be a very important player for us at that time of the season. That was the reason.
“It is disappointing for Zoran but there is nothing we can do about it. There have been others left out.”
