Ferguson was left upset by the manner of Bayern's eventual success.
"I don't think the best team has won the tie, I think we played better tonight than they did," he said.
"I don’t think anything’s been missing in our campaign, and I don’t think we were fatigued tonight. With them having the extra man, they made the ball work. We defended very well and it’s taken an exceptional goal to finish the tie. It was a tremendous hit by [Arjen] Robben.
"I think we’ve done well. Our performance tonight was excellent, it was a great performance. We were very unlucky tonight, very, very unlucky."