City came out with all the belief of a team that is yet to taste defeat in the Premier League so far this season, with Bernardo Silva firing narrowly wide before United had even managed to touch the ball.
The hosts continued to knock at the United door in the opening exchanged and were rewarded for their endeavours as they took the lead with just 12 minutes gone.
Raheem Sterling's cross to the far post was kept alive by Bernardo Silva and as the ball came back across the face of goal David Silva was the first to react to cut inside a challenge and rifle home.
City's dominance continued for the remainder of the half, with Pep Guardiola's men very much in control of the ball, albeit without carving United open with any real regularity.
A rare United foray forward saw Chris Smalling's tame, looping header land on the roof of the net, before Aguero found the side-netting on the stroke of the break following Bernardo's through ball as City looked for a second.
That search didn't need too long after the interval, though, as City doubled their lead with 48 minutes on the clock.
The hosts seized on a loose ball in midfield before Bernardo once again fed Aguero, this time just inside the United half.
The Argentine drove forward, drawing the United defence before exchanging passes with Riyad Mahrez and thundering an effort beyond a helpless David de Gea and into the roof of the net at the near post.
His eighth goal in a Manchester derby, the strike saw Aguero move level with Wayne Rooney as the fixture's joint-top scorer in the Premier League era.
November 11, 2018
However, an inspired substitution from Jose Mourinho threatened to turn the game on its head as Romelu Lukaku was felled by Ederson in his attempts to round the Brazilian just 30 seconds after coming off the bench, leaving Anthony Taylor with no option but to award a penalty.
The in-form Anthony Martial took responsibility from the spot, keeping his cool to send Ederson the wrong way and become on the fifth Frenchman to score in five consecutive Premier League games.
United briefly threatened to mount another of their recent second-half comebacks, but City soon wrestled back control of the game and went about closing it out.
Substitutes Leroy Sane and Gundogan both screwed efforts wide when found in decent positions, but the German made amends as he made the game safe with four minutes to play.
It was vintage Gundogan as he snuck in on Nemanja Matic's blind side to control Bernardo's right-wing cross and slot beyond de Gea from close range to cap a 44-pass move and secure Manchester bragging rights.
The win sees City move back top of the Premier League two points ahead of Liverpool going into the international break, whilst United remain below Watford and Bournemouth in eighth.
November 11, 2018