Berbatov was unable to play any part in United's 1-1 draw with Birmingham at St Andrew's as they were unable to achieve the victory which would have taken them above Chelsea.
Instead Ferguson gave a debut to summer signing Mame Biram Diouf who came on as a second half substitute.
Ferguson said: "Dimitar wanted to play with it but we felt we should try to get it (the knee) sorted and get him fit again.
"He may have to have an exploratory operation."
Ferguson reiterated his anger at Darren Fletcher's red card by referee Mark Clattenburg with the second yellow awarded for an innocuous trip on Jerome.
The United boss said: "You won't see a softer sending off. For a start, Darren's not that kind of player.
"It's a simple clip on the boy (Jerome) who actually stumbled. I think it was a terrible decision and it gave Birmingham some momentum.
"But I think we've got to be satisfied with a point particularly as we've ended the game with 10 men.
"Birmingham is a difficult place to go and they are playing very well. It is not a bad point."
Ferguson was not unhappy with a share of the spoils against a Blues side who have now gone a club record 12 league matches without defeat particularly after Fletcher's dismissal for two bookable offences.
United needed an own goal from City defender Scott Dann to collect a point after Cameron Jerome had given the home side an undeserved half-time lead against the run of play.
Ferguson said: "We were down to 10 men for the last part of the game but in the first half we played absolutely brilliantly and dominated the match.
"It was a travesty to go in at half-time 1-0 down after they scored with their first attack.
"It was a sickener but it's important not to let your head go down. We kept battling away and deserved a point.
"We spoke about remaining patient at half-time because 45 minutes is a long time.
"We've won so many games late on so we shouldn't worry about being 1-0 down. We've faced that situation many times."
After dominating the opening 45 minutes, United were indebted to some fine second half saves from Tomasz Kuszczak for earning them a point.
But the former West Brom goalkeeper was frustrated at United's failure to get back on the winning trail after their shock FA Cup reversal against Leeds.
He said: "We're disappointed, of course. We came to Birmingham for three points and only drew the game.
"We know what we have to do to keep up our challenge for the title and we want to win every match, no matter who we play.
"If we lose some points we are disappointed. We had most of the possession in the first half and created some chances. They were lucky to get the goal, but this is football.
"We scored in the second half but Birmingham defended very well and made it difficult for us. We had some chances but couldn't score again."
Kuszczak played down his own contribution including a late reflex save to deny Birmingham defender Roger Johnson a winner.
He said: "This is what I have to do. I play for the biggest club in the world and always try to give 100 per cent, help the lads win the game and keep a clean sheet.
"I didn't manage it, and although I made some saves, it's still disappointing we didn't win."end
Source: Manchester Evening News