Aguero, who opened the scoring after just 46 seconds, netted all three from close range as City bounced back from their midweek defeat Newcastle with a convincing display at the Etihad Stadium.
Arsenal did pose some awkward questions after finding a quick equaliser through Laurent Koscielny, but two more from Aguero either side of the break put the result beyond doubt.
There was an element of controversy over Aguero's third after the ball struck his arm as he bundled it in, but it was not deemed deliberate.
City eased through the final stages to put the onus on Liverpool to respond at West Ham on Monday.
Ederson - 8 out of 10
Came off his line superbly to beat Aubameyang to the ball. Little he could do to prevent Koscielny’s equaliser.
Kyle Walker - 6 out of 10
An improvement on some recent performances. Comfortable when in a back three after playing the same role with England.
Nicolas Otamendi - 6 out of 10
A forceful presence at the back, sometimes too forceful. One robust first-half challenge on Lacazette went unnoticed.
Aymeric Laporte - 7 out of 10
Picks up a rare assist, crossing for Aguero’s first, then saw a goal disallowed for offside. Covered well for Sterling, who was alone on the left flank.
Fernandinho - 7 out of 10
Initially struggled to exert his usual control over the midfield in the first half, perhaps because he had to keep dropping back into defence, but improved.
Bernardo Silva - 7 out of 10
Out of position on the wing and less influential than he often is in a central role but still troubled Arsenal’s left side.
David Silva - 7 out of 10
Not masterful from Il Mago but an all-round improvement on his display at St James’ Park, sprinkled with the odd special touch or pass.
Ilkay Gundogan - 8 out of 10
Almost faultless when distributing the ball. A delicate chip over the top of the defence in the build-up to Aguero’s goal was his best.
Kevin De Bruyne - 6 out of 10
Did not have his usual influence on the game. An off-day though hardly anything to be concerned about.
Raheem Sterling - 8 out of 10
Created two of Aguero’s three, ghosting superbly behind Lichtsteiner for the second. Asked to cover the entire left flank but did not look out of place.
Sergio Aguero - 9 out of 10
Header, right foot, left arm. An unconventional hat-trick but his 14th in City colours. The wrong side of 30 now but his predatory instincts have not waned.
Bernd Leno - 6 out of 10
Dives too early and the wrong way for Aguero’s first but denied City impressively on several occasions after it.
Stephan Lichtsteiner - 5 out of 10
Caught out by Sterling’s intelligent movement, particularly on City’s second. Arsenal’s third-choice at right back and it showed.
Laurent Koscielny - 5 out of 10
Equalises from Torreira corner, Monreal flick-on, but culpable for letting Aguero go at the far post for City’s crucial second.
Shkodran Mustafi - 6 out of 10
Five yards behind the rest of the Arsenal defence for Aguero’s first, playing every City player onside, though perhaps did not anticipate Iwobi’s error.
Nacho Monreal - 7 out of 10
Neat near-post flick-on for Koscielny’s equaliser. Coped well enough with Bernardo despite being given little support.
Alex Iwobi - 5 out of 10
Dispossessed deep in his own half by Laporte. Attempted to make up for his mistake and was tidy enough, though did little to atone.
Matteo Guendouzi - 7 out of 10
Poor start but did not hide and grew into the game as it went on. Largely shut down City’s midfield with Torreira until the game got away from Arsenal.
Lucas Torreira - 8 out of 10
Made several key interceptions and tackles, especially as momentum shifted towards Arsenal in the first half.
Sead Kolasinac - 6 out of 10
Stationed at left midfield but perhaps too adventurous for his full-back’s liking, with Monreal left one-on-one with Bernardo too often.
Alexandre Lacazette - 6 out of 10
Him and Aubameyang were sat strangely deep, bulking up Arsenal’s midfield, and this affected his ability to get forward.
Pierre-Emerick Aubameyang - 6 out of 10
As with Lacazette, often too deep to threaten, though a little brighter than his partner and Arsenal’s main threat on the counter-attack.
Additional reporting by PA
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