Berbatov, a £30 million signing from Tottenham Hotspur in 2009 and the joint leading scorer in the Premier League this season, wasn't expected to start the game, which United lost 3-1, but failed even to make the bench.
Early reports suggested Berbatov had left Wembley after being told of his omission and the Sunday newspapers are full of speculation about the Bulgarian's future, or lack of it, at Old Trafford.
However, Ferguson insists that Berbatov did not throw a wobbler and was in the United dressing room after the final whistle. The United boss also said his decision to leave out the 30-year-old had prompted "heartache" in the build-up to the match.
"For Berbatov it was a difficult decision," said Ferguson. "Picking my team I found easy, but picking my subs I found very difficult. I tended to overload the midfield positions because I thought that was the position that was most important.
"I gambled with just one defender (on the bench) to allow me to get as many options in midfield and wide positions. It was a choice between Michael Owen and Dimitar Berbatov and if you are looking for someone to nick a goal in the last few minutes you want Owen's experience."
Berbatov is entering the last year of his contract at Old Trafford and he has been linked with a return to Tottenham.