The Argentinian’s glancing header gave City a first half lead at the Etihad, and his penalty doubled their advantage after the break.
Jacob Murphy got the visitors back into the contest with a brilliantly-taken goal, racing away from the Premier League leaders’ backline before beating Ederson.
But despite their late endeavours, Rafa Benítez’s side couldn’t produce a leveller, and Aguero’s third of the day with just under ten minutes left sealed the points.
The Magpies began with a back five, as midfielder Isaac Hayden dropped deep to partner Jamaal Lascelles and Ciaran Clark in the heart of defence.
They made a positive start with Paul Dummett finding space to cross on the left, though when the ball fell for Clark, he couldn’t quite make a clean connection and Ederson gathered.
John Stones turned one wide at the other end and Kyle Walker skied one, but from then on it was the hosts who enjoyed the majority of the play. A swift counter-attack from City resulted in Raheem Sterling tapping home Leroy Sane’s cross, but it was ruled offside and United survived.
Pep Guardiola’s table-toppers didn’t register a shot on target until just after the half hour mark when Sterling shot straight at Karl Darlow, but just a few minutes later, they seized the advantage. It had been coming, but it was no less disappointing for Newcastle, who had held firm until then. Kevin De Bruyne’s inswinging cross was met by Aguero, and he got the slightest of touches on it to help it on its way into the corner.
Darlow denied De Bruyne with a smart save before the break, and the Belgian and Aguero both went close before City continued to push after the break, with Lascelles producing a fine sliding challenge to prevent Sane from getting a shot in.
A similarly timely intervention from Hayden averted what would have been a tap-in for Agero, but just after the hour the pressure told once more. Sterling burst into the box and was adjudged to have been pulled back by Javier Manquillo, and Aguero hammered home his and his side’s second from the spot.
But Newcastle showed some fight, and Murphy’s first goal for the club reduced the deficit with 66 minutes on the clock. Clark’s superb searching pass bypassed full back Oleksandr Zinchenko and allowed the former Norwich City winger to home in on goal and apply a delicate chipped finish to pull one back for Benítez’s men.
Sterling remained a threat at the other end, though, and Darlow pulled off an excellent stop to turn the England international’s shot onto the base of the post.
United, buoyed by Murphy’s goal, responded and Mo Diamé’s surge into the box was only halted by goalkeeper Ederson, who palmed away his effort and smothered the midfielder’s rebound.
But Guardiola’s side wouldn’t be kept quiet for long. Sane’s cutback from the left was met by Aguero, who swivelled before firing home on 83 minutes to claim the matchball and the three points for his team.
