Although City had lost their previous home game to Lyon in the Champions League, there was never much chance of a repeat against a Brighton side who have never beaten them away.
City have now dropped just four points from their past 39 in the league.
Raheem Sterling opened the scoring with a simple tap-in for his fourth goal of the season after excellent work from Leroy Sane on the left.
Sterling was also involved in City's second, exchanging a superb one-two with Aguero after the Argentine had burst forward from the halfway line, beating three players on his way.
Aguero kept his cool to slot home for the win that returned City to the top of the table ahead of the late kickoff between Chelsea and Liverpool.