The victory put the pressure on Liverpool ahead off their trip to West Ham United on Monday. Juergen Klopp’s side have 61 points with champions City on 59 and Tottenham Hotspur on 57.
City were utterly dominant after going in 2-1 up at the break, keeping Gunners keeper Bernd Leno busy as they peppered his goal with shots from distance while the Londoners, looking bereft of self-belief, did not manage a shot on target in the second half.
Pep Guardiola’s side needed a positive response after Tuesday’s surprise defeat at Newcastle United and within a minute any nerves among the home crowd vanished.
It took 48 seconds for Aguero to open the scoring with a stooping header after Aymeric Laporte had robbed a far-too casual Alex Iwobi and whipped in a cross.
City were dominant but the Gunners got back on level terms in the 11th minute when Nacho Monreal flicked on a Lucas Torreira corner and defender Laurent Koscielny headed in from two yards out.
But with Kevin De Bruyne beginning to put his injury troubles behind him and looking like his true self in midfield and Bernardo Silva teasing Arsenal from the right flank, City looked unperturbed by the equaliser.
It was no surprise when 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.
De Bruyne forced three saves out of Leno in the opening 10 minutes of the second half before City finally made their dominance count.
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 — a fact the player conceded after seeing the television replay.
“I thought it was the chest, but now that I’ve seen it on the TV, I think it was a handball,” he said.
“I’m very happy, it is important to score and win… It’s important to fight every game. Now we have to think about Everton (on Wednesday) because it will be so difficult,” he added.
It was Aguero’s 10th hat-trick in the Premier League, 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.
Guardiola believes City now face greater pressure than rivals Liverpool.
“I prefer to be in Liverpool’s position rather than where we are,” he said.
“The pressure is when you’re behind. If you lose points it’s tougher. When you’re top with distance you can lose points and still be there.
“We didn’t recognise our team against Newcastle. Today at least we came back,” Guardiola added.
Arsenal boss Unai Emery accepted the scoreline reflected the difference in quality between the teams.
“They showed their superiority today. They showed today with the possession against us, getting our defence position very deep….. The result is the difference between us,” he said.