Pep Guardiola’s side, who were again without the benched Joe Hart took the lead through David Silva, despite two Aguero penalty misses.
Aguero managed to eventually find the net before the break with Nolito getting his first City goal minutes into the second half.
The Argentine added his second and third to atone for his earlier misses as City romped home in impressive fashion ahead of next week’s second leg.
Despite leaving around £109m worth of talent at home, Guardiola’s side shot out of the blocks with a rejuvenated Raheem Sterling winning a seventh minute penalty as Muniru Sulley brought him down.
However, Aguero missed the opportunity to score his second spot kick in as many games with Nolito thumping the follow-up against the crossbar and out.
On 13 minutes Sterling showed a great show of pace to rob Alin Tosca of the ball and set up Silva to break the deadlock from close range.
Not satisfied with one, City pushed hard for a second and Aleksandar Kolarov won them yet another penalty on 20 minutes.
Unbelievably, inconceivably, Aguero missed again from the resulting spot kick though, hammering the ball over the bar.
Kolarov struck the bar on 38 minutes before Aguero finally found the net with a beautifully placed shot from a classy Sterling set up to make it 3-0 at half time.
And it was more of the same after the break as Nolito rounded the goalkeeper to add a third after an eye-of-the-needle pass by Kevin De Bruyne.
Aguero made it four with ten minutes remaining after an intricate passing move involving Nolito before the Argentinian bagged his second.
With two minutes of the 90 left, Aguero completed his eighth Manchester City hat-trick with his low shot hitting the post and nestling into the corner of the net to complete the rout.