He has scored just eight times in 27 league appearances while his miss, after coming on as a substitute, in Sunday's FA Cup semi-final penalty shootout defeat by Everton proved critical as United's quintuple dream bit the dust.
In the build-up to that match, the United manager has defended Berbatov from accusations he is is not living up to his exorbitant transfer fee.
"I don't see any evidence of that," said Ferguson. "He has had his injuries but I thought he did well when he came on in the semi-final.
"He was disappointed to miss his penalty and he'll get criticism for that.
"When you pay 30 million pounds for a player everyone thinks he should be able to score a penalty kick. But anyone can lose on penalty kicks.
"Berbatov was upset but then it was a disappointed dressing room, you'll always get that after a semi-final (defeat).
"And it was our first semi-final we've lost, don't forget that. We've got to move on.
"We've done it in the past and we'll do it again," said the veteran United manager, who fielded a largely second-string side against Everton.
Ferguson remained defiant despite having seen the club's hopes of an amazing clean sweep of trophies go out of the window at Wembley.
He fully expects to see his side bounce back against Portsmouth and keep the pressure on title rivals Liverpool, who are in action against Arsenal at Anfield on Tuesday where a draw will see them overtake United at the top of the table before United kick-off against Pompey.
"We have to overcome defeats at some point and in most cases we have done alright," added Ferguson.
"I think there is enough motivation among our players to look forward to the game," he insisted.
"Trying to deal with the tiredness after Wembley, especially after extra-time, was always going to be the issue," said Ferguson.
"But there is enough freshness in the rest of the squad to be alright on Wednesday, that's how we planned it."
"It's a blow because he's been doing really well for us and he's an important part of what we do," said manager Paul Hart.
Portsmouth, who dumped United out of the quarter-final stage on their way to winning the FA Cup during their last visit to Old Trafford 13 months ago, head for Manchester knowing that 17 of their players are out of contract at the end of the season.
"At the moment, we are just concentrating on staying in this division," said Hart, whose side are six points above the relegation zone with six games to play.
"Contracts will be discussed at the appropriate time - but it's not right now," Hart explained.
Source: AFP Global Edition