The defending champions are now two points behind leaders Liverpool.
The victory put the pressure on Liverpool, ahead of their trip to West Ham United on Monday.
Juergen Klopp’s side have 61 points, with champions Manchester City on 59 points and Tottenham Hotspur on 57 points.
Aguero gave Manchester City the lead after 48 seconds with a stooping header, after Aymeric Laporte had robbed Alex Iwobi and whipped in a cross.
Manchester City were dominant, but the Gunners got back on level terms in the 11th minute.
That was when Nacho Monreal flicked on a Lucas Torreira corner kick and defender Laurent Koscielny headed in from two yards out.
Aguero struck again just before the break, tapping in a low cross from Raheem Sterling, who had combined well with Ilkay Gundogan in the build-up.
Manchester City’s record scorer wrapped up the win, with Sterling again the provider.
But as Aguero slid in to meet his low cross, the ball appeared to go in off his arm.
It was Aguero’s 10th hat-trick in the EPL, a record bettered only by Alan Shearer who scored 11.
The Argentine striker has netted 20 goals in all competitions this season — the sixth straight campaign he has reached that tally.(Reuters/NAN)