Rooney missed United's 4-3 win over Newcastle on Wednesday afternoon and Ferguson confirmed the striker will miss the remainder of the festive programme.
"It was a volley towards the end of training," said Ferguson.
"He did a ligament at the back of his knee and could be out for two to three weeks."
Rooney will miss Premier League matches against West Brom and Wigan, in addition to the FA Cup third round tie at West Ham on January 5.
He also faces a race against time to face Liverpool at Old Trafford on January 13.
And for Ferguson it was a particularly disappointing given Rooney's poor performance at Swansea on Sunday.
"After his performance on Sunday I think he would have been brilliant today [Wednesday]. You don't have two performances like he did on Sunday," said Ferguson.
"Unfortunately we couldn't risk him."
It was part of a negative fitness bulletin from the Red Devils boss, even if details of exact injuries were sketchy.
"Danny Welbeck took ill in the team hotel last night," he said.
"Ashley Young also got injured yesterday [Tuesday] and Phil Jones got injured against Swansea."
And, while skipper Nemanja Vidic was on the bench on Wednesday, Ferguson did not want to use him after the centre-back made his first start since September at the Liberty Stadium.
"We couldn't risk Vida after playing his first game," said Ferguson.
"He had a bit of soreness in his knee, which is only to be expected after being out for so long."