United made it a record 20 Champions League matches unbeaten, although Fergie sprung a surprise by starting with Wayne Rooney on the bench.
Jonny Evans played despite an ankle injury but Ferguson revealed he had made plans to cover for the defender's absence.
The Sun quoted him as saying: "I felt we would have a weakness in our aerial defending set-piece plays without Jonny and I had to have Dimitar Berbatov in.
Mourinho failed to shake hands with Fergie at the end.
But the former Chelsea boss explained: "My dugout has a door that gives me a chance to leave immediately.
"Yesterday I left Sir Alex a bottle of wine at his hotel with a card to say we will see each other at Old Trafford after the game. I am always friends with him."