The striker has been ruled out for between two and three weeks with the problem, which kept him out of a thrilling Boxing Day victory over Newcastle.
Rooney's replacement Javier Hernandez scored an injury-time winner in a 4-3 success which put United seven points clear at the top of the Premier League.
And after the game Sir Alex Ferguson told MUTV the reason for Rooney's omission from the 18-man squad.
He said: "It was a volley towards the end of training. He did a ligament at the back of his knee and could be out for two to three weeks."
Ferguson's worst-case scenario would see the England international miss Premier League games against West Brom, Wigan and Liverpool and the FA Cup third round tie at West Ham.