The £30.75million man netted his first United goals to add gloss to the scoreline after Wayne Rooney's first-half opener.
The only negative for United was a knee ligament injury for Paul Scholes.
Rafael Da Silva was in impressive form and showed a willingness to get forward, starting the attack which saw Nani blast a shot at Aalborg skipper Thomas Augustinussen.
And there were only five minutes on the clock when Berbatov fired wide of an open goal.
And it was Giggs who laid on the opening goal on 22 minutes. The Welshman collected a short pass from Nani before feeding through an inch-perfect pass for Rooney to take in his stride and slot home from inside the penalty area.
Andreas Johansson failed to get his header on target as he tried to turn home Martin Pedersen's cross, then Nani came agonisingly close to netting another for the visitors.
United made it 2-0 after a horrendous mistake from Augustinussen.
The defender failed to control a routine square ball on the edge of the box and Berbatov made no mistake lashing the ball into the net with 55 minutes gone.
Nani then got away down left and his shot was saved by Karim Kaza before sub Carlos Tevez converted the loose ball, but the goal was chalked off for handball.
United were breaking through the Aalborg defence at will and Cristiano Ronaldo got away down the right before chipping the ball in for Berbatov (79), who acrobatically volleyed in his second of the night.