The Red Devils defeated English rivals Chelsea 6-5 on penalties after it had ended 1-1 at the Luzhniki Stadium in Moscow.
Speaking to MUTV after being confirmed as the manager of the MUFC 2008 XI for Michael Carrick's June testimonial, Ferguson spoke of his major regret of that European triumph.
"Well, to win the European Cup is fantastic," said Sir Alex.
"It was a really great bunch of players with a great attitude about them and a good, strong squad.
"My problem in the 2008 final, maybe I even regret it to this day, was I left Ji-sung Park out completely in the final. He'd played such a great role and that's the problem when you get to these finals.
"At Wembley [against Barcelona two years later], I did it to Dimitar Berbatov and he took it badly. He didn't deserve it. No player deserves to be left out of the final. That's why we try hard at these European seminars with the coaches to try to get 11 subs in the final.
"You've got four or five sitting in the stand who made fantastic contributions in getting there. You start the tournament in September and go through to May and changes can happen. Maybe you sign a player in January, for instance, who can end up playing in the final.
"It's a difficult part, always, picking a team for the final in Moscow and I had to make that horrible decision."