The Bulgaria striker, who had failed to find the net in three previous appearances for the Red Devils following his £30million transfer deadline day arrival from Spurs, spurned a gilt-edged chance to fire his new side into an early lead before making amends.
Berbatov capitalised on a defensive howler for his first goal on 55 minutes then acrobatically volleyed home his second 11 minutes from full-time.
Wayne Rooney had opened the scoring for Sir Alex Ferguson's side before limping off on the hour-mark with a leg injury.
United started strongly and always looked capable of opening up a shaky home defence.
Indeed, Berbatov held his head in his hands when he blazed a sixth-minute volley wide of an open goal after Cristiano Ronaldo had charged down a clearance from the goalkeeper.
Rio Ferdinand also saw a powerful shot from a flicked on corner deflected behind by a combination of keeper and defender before United took the lead in the 22nd minute.
Ryan Giggs, who had arrived as an early substitute for knee injury victim Paul Scholes, picked out the run of Rooney in behind his marker and the England striker coolly slotted the ball home from 15 yards.
United continued to hold the upper hand and carve out the clearest opportunities, but they had to wait until Aalborg's legs began to tire in the second half to increase their advantage.
Even then the goal came in fortuitous circumstances as Thomas Augustinussen gifted a chance to Berbabtov with some woeful control and, when the ball looped up to the striker, he gleefully rammed a simple shot into the back of the unguarded net.
Substitute Carlos Tevez saw a 61st minute bundled effort ruled out for handball, before Berbabtov claimed his second and United's third of the night with 11 minutes remaining.
Ronaldo reached the byline and cut the ball back to where Berbatov was waiting to execute an athletic volley on the turn past the helpless keeper, to complete the scoring on a straightforward night for the holders.