After coming off the bench to influence the Gunners' win over Cardiff City in their last league outing, Unai Emery restored the Nigeria international into his starting line-up, playing on the right wing in the attack of a 3-4-3 formation.
The hosts went ahead after only 48 seconds into the game, with an indecisive Iwobi the culprit.
The 22-year-old was dispossessed by Aymeric Laporte on the edge of the box - as Arsenal sought to clear their lines - before the ball was worked to Aguero who converted with a diving header.
10 minutes later, against the run of play, captain Laurent Koscielny restored Arsenal's pride, heading off a corner kick.
Pep Guardiola's side went into the break with a lead, though, as Aguero scored off a well-worked move from the right side of the visitors' defence.
The Argentine claimed his hat-trick after the restart, with the majority of the work coming off Arsenal's overexploited right wing.
Iwobi - who won only 27.3% of his duels - also failed to inspire any confidence in Arsenal's attack, registering no shot and attempted just 18 passes.
He was, however, put out of his misery in the 66th minute, with Aaron Ramsey taking his spot as Guardiola's charges were prevented from doing more damage.