Pep Guardiola's side had faced the prospect of falling seven points behind Liverpool after Tuesday's shock 2-1 loss at Newcastle United, but the league leaders could only manage a home draw with Leicester City the following day.
And with Jurgen Klopp's charges not in action again until Monday's trip to West Ham, City got to within touching distance of the summit as Aguero broke the deadlock after just 46 seconds.
Laurent Koscielny's leveller against the run of play reminded City of their opponents' quality, but unlike at St James' Park – when Aguero's goal after just 24 seconds came in a losing effort – the reigning champions bounced back to wrap up the points.
Aguero took the match ball with two close-range finishes, the latter having hit his arm, to ramp up the pressure on the Merseysiders and keep Arsenal in sixth, three points adrift of the Champions League spots.
City started the match in third spot following Tottenham's victory over Newcastle but had won their last four home games with an aggregate score of 24-0, and another three points seemed inevitable after Aguero's early stooping header from Aymeric Laporte's cross.
Indeed ,Guardiola, who has never lost a match to Arsenal boss Unai Emery in all competitions, saw his side make a barnstorming start and Aguero had a penalty appeal waved away following contact from Shkodran Mustafi before Raheem Sterling stung the palms of Bernd Leno.
An offside flag cut short celebrations when Laporte nodded in Kevin De Bruyne's free-kick, but a seemingly beleaguered Gunners side hit back when Nacho Monreal flicked on Lucas Torreira's corner and Koscielny headed in.
Ederson had to be alert to clear from in front of Pierre-Emerick Aubameyang as he looked to get on the end of Alexandre Lacazette's throughball, with the visitors evidently growing into the contest.
But their hard work was undone a minute before the interval as Aguero tapped home from Sterling's low cross.
The hosts sought to put the game to bed in the second half and De Bruyne should have done better at the end of a swift counter-attack in which he had played a key role, but the Belgian's finish was tame.
It took until after the hour mark for City to end Arsenal's hopes, Aguero getting the scruffiest of goals after the ball struck his arm as he slid in when Leno failed to collect Sterling's cross.
A late Denis Suarez debut cameo did little to lift the Gunners' gloom and City will now watch Liverpool's trip to West Ham with interest.
What does it mean? City title tilt back on track
The defeat at Newcastle, though somewhat mitigated by Liverpool's slip-up 24 hours later, was a shock to the system for a City side who were uncharacteristically lacklustre in midweek. This showing was far more befitting of champions and once more the pressure is back on Liverpool.
Aguero the goal machine
Does Aguero always get the credit he deserves? A prolific striker in the Premier League season after season, and yet who raises his name in conversations about modern greats of the game? This treble moved him onto 157 top-flight goals for City and you can be sure there are more to come.
Kolasinac lacking tactical discipline
When you visit the Etihad, you have to be prepared to do a great deal of work without the ball, but Sead Kolasinac did not seem up for that. Despite ostensibly being deployed as a left wing-back, the German's average position was higher up the field than Lacazette. His passing accuracy of 52.6 per cent will also have contributed to Emery's decision to take him off after 66 minutes.
Key Opta facts
- Manchester City have won four consecutive top-flight games against Arsenal for the first time since April 1937.
- Since the start of 2018, only two teams have lost more away games than Arsenal (12) in the Premier League – Brighton (14) and Huddersfield (13).
- Manchester City have won eight of their nine games in all competitions in 2019 (L1), scoring 34 goals and conceding just four in return.
- Aguero has been directly involved in 27 goals in his last 15 home starts in the Premier League (22 goals, 5 assists).
- At the age of 24 years and 57 days, Sterling has become the seventh youngest player in Premier League history to register 100 goal involvements in the competition (59 goals, 40 assists).
- 50 per cent of Manchester City's goals conceded in the Premier League this season have been from set pieces; the highest ratio in the division (10/20).