Ferguson revealed Scholes, who has been struggling with the problem and sat out of the midweek trip to Real Madrid, will not be available for Monday's FA Cup tie with Reading.
"It is a knee injury, which has been bothering him a bit," said Ferguson. "We have tried another treatment during the week. He will probably be back in another couple of weeks."
Ferguson also confirmed that United had suffered no fresh injuries in their impressive 1-1 draw at the Bernabeu.
“We've come through Wednesday night's game without any injuries,” he said. “That's the best thing, apart from the result of course.
"Of course, I'll make some changes for Monday night, even though it’s an incentive to get to the quarter-final. I don’t think that’s lost on any of the players.
"I think there's a good spirit in place and they're all contributing. Whatever side I pick we’re expected to qualify. That's what happens at United. Whatever team you play you’re always expected to win.
"I went to see Reading last week and they’re a team who are showing plenty of fighting qualities at the moment, as you’d expect given they’re down the bottom of the league.
"We'll take nothing for granted. In the FA Cup you always expect the unexpected. It happens so many times. You just hope you're not a casualty or a shock. We've had a few over the years."
Meanwhile, Ferguson said he is happy for Vidic to inch his way back, and believes he is right to limit the defender's game time at the moment.
"Steadily, he's getting there," he said. "He was fantastic against Everton and I had my doubts over whether I was doing the right thing or not.
"But, in my mind, three days' recovery was a risk, so I stuck by what we've been doing with him.
"We've managed it for a while now. When Nemanja came back from his latest injury he'd only played about eight games in 18 months. That's a long time out and not a lot of games."