Ferguson: Poor possession proved costly
Bayern clinched a last-gasp victory in the first leg of the quarter-final when Ivica Olic netted in the dying seconds after United scored first when Wayne Rooney volleyed home in the second minute.
"We scored early but I don't think we started well at all," Ferguson told reporters.
"The disappointment for me tonight was we gave away the ball too easily. Our possession of the ball was not up to our standard. This is something we pride ourselves in," the Scot said.
United looked to be on track for another away win but Bayern gradually balanced out the tie as the visitors struggled to come forward in the second half.
Ferguson brought on Dimitar Berbatov in the 70th minute to help control the ball but it made little difference.
A deflected Franck Ribery free-kick made it 1-1 before Olic scored the winner from close range.
"The real crux of the battle was giving the ball away," Ferguson said. "We did not need to work for the goal. It came too easily."
"We had outstanding chances to kill the tie through Rooney," Ferguson said. "That would have been lucky for us. (Keeper Edwin) Van der Sar time and time again made some fantastic saves and kept us in the game."
Ferguson said United still had a good chance of advancing to their fourth consecutive semi-final with the return leg in Manchester next week, despite their first away defeat in the competition this season.
"It is always an advantage to score away from home so the tie is not dead. We have a strong chance. We should have a real chance of progressing but it is very tight," Ferguson said.