Ferguson said that Chelsea were the better side in the second half and insisted that the midweek defeat to Real Madrid left his players tired as the game went on.
"We're lucky to still be in the cup," the Scot told MUTV. "We just ran out of legs and Chelsea were far the better team in the second half.
"But I can't be critical of my side because the running they had to do on Tuesday night against a really top side in Real Madrid, had its bearing on today's result, no doubt about that.
"The two full-backs, Rafael and Patrice [Evra], are knackered and the two central midfielders tired badly. We kept giving the ball away and it made it a long day for us, going from one penalty box and back to our own."
The winner of the replay at Stamford Bridge will face Manchester City in the semi-finals.