The Brazilian had just got back into the side after being sidelined for over a month, but he had to be replaced by Park Ji-sung inside the opening 20 minutes.
Scans have shown the 21-year-old has suffered severe damage to his cruciate ligament and he will play no further part in United's campaign.
"The real bad news is that Anderson has a cruciate knee injury," said Ferguson. "He will be out for the rest of the season. It is a bad blow.
"He was looking forward to the match on Tuesday and he was showing great energy to do well.
"It is a bit of a blow to us, particularly with the AC Milan game coming up because Michael Carrick is suspended.
"It is strange, when you see cruciate injuries it is usually something simple. He stretched out for the ball and his knee just popped.
"We have assessed the situation and know he needs the operation.
"That will be done in two weeks' time in Portugal once the swelling has gone down. Sometimes we have sent them to Dr Steadman in Colorado. In this instance he is comfortable with the surgeon he has dealt with in Portugal in the past.
"He will be out for six months and hopefully that should have him about right for the new season."