Milan were their own worst enemy after failing to put away a host of chances in the first half, Ronaldinho, Alexandre Pato and Klaas Jan Huntelaar being the main culprits.
England international Beckham said: "If in the first half we'd scored the goals when we had the chances, then it would have been a different game.
"But we didn't and Manchester United are a very good team and Wayne Rooney is a very good player."
Clarence Seedorf pulled a late goal back for Milan with Beckham commenting:
"Clarence's second goal has made it possible. It's not easy to go to Old Trafford but we've made it a bit better for ourselves.
"If we'd come off the field having lost 3-1, then we'd have been more disappointed."