The two sides meet again next Thursday in Denmark but Mark Hughes will be delighted with his side's performance and they will enter the away leg with confidence in their two-goal lead.
Felipe Caicedo opened the scoring after just eight minutes when he brilliantly turned on Michael Jakobsen and slotted past the despairing keeper to give City the dream start they were looking for.
There were chances at either end in the aftermath of the goal, with Robinho a constant threat for the home side and Caca making Shay Given work in City's goal. But City doubled their advantage on 30 minutes through Shaun Wright-Phillips' impressive solo effort.
City outshone their opponents for much of the first half but had to rely on some poor Aalborg finishing in the second to protect their two goal cushion, as the Scandinavians showed their ability to pass and move on the counter attack.
It should be more than enough though, as City try to emerge from a difficult season by ending a trophy drought stretching back to 1976.
FormWhile City have been a model of inconsistency on the domestic front this season, Europe has tended to bring out their best form.
And so it proved again with a performance that was far too good for an Aalborg side competent enough to hold Manchester United at Old Trafford in the UEFA Champions League last December.
What a pity therefore that so many City fans have opted to turn their backs on the tournament.
The swathes of empty seats in a barely half-full stadium could be down to a number of factors, not least a third meeting against a Danish club in City's run to the last 16.
With record signing Robinho back from an ankle injury, Hughes had a joyous array of attacking weapons at his disposal, especially as in the absence of Vincent Kompany and Nigel de Jong, the Blues had more playmakers in the centre of the park than would normally be the case.
The contest was only eight minutes old when Caicedo opened their account.
The Ecuador striker has twice been tipped to leave City after failing to make much of an impact since arriving halfway through Sven-Goran Eriksson's brief reign.
But loan deals to Hertha Berlin and Fulham fell through during consecutive transfer windows and with so many forwards on the treatment table, Caicedo has proved a handy man to have around.
And there was certainly nothing shabby about his finish after he had collected Robinho's square ball and held off Jakobsen before beating Karim Zaza.
If Caicedo is a relative newcomer in first-team circles, Wright-Phillips has been around for a long time.
StruggleAalborg struggled to contain the England star from the first whistle and when Stephen Ireland provided the killer pass, Wright-Phillips left Patrick Kristensen for dead before beating Zaza with an almost languid strike that nevertheless had too much power to be prevented from ending up in the top corner.
Had referee Alain Hamer spotted a clear foul on Robinho by Michael Beauchamp, who had been flummoxed by half a dozen stepovers close to the six-yard line, the tie would have been over.
Not that it made much different to the Blues' attacking attitude as Nedum Onuoha was inches away from nodding home Elano's corner before a Robinho snap-shot brought the latest in a series of good saves out of Zaza, who had already bravely denied Micah Richards.
On home soil, against opponents incapable of exerting any pressure in the midfield area City might have been vulnerable, the hosts continued with their glowing brand of football, each individual producing a memorable moment to bring the fans lucky enough to witness it, to their feet.
Elano's influence was growing and the former Shakhtar Donetsk man provided Wright-Phillips with an excellent shooting opportunity when he split the Aalborg defence, only for the chance to be wasted as the winger fired wide.
Aalborg did manage one final flurry, during which Kasper Risgard floated a free-kick over and Caca screwed a decent opportunity badly wide.
But a goal at that stage would have been an injustice as City sense a place in the last eight.
1st Half Goals
Shots on Target
Shots off Target