The 30-year-old opened the scoring in the first half as he drilled home low from the edge of the box following good work form Phil Foden to bring up his 200th goal for the club but he clearly had no intention of stopping there.
Just before the hour mark, a Chelsea move broke down deep in the City half and they were ruthlessly picked off on the counter.
Pep Guardiola's side drove forward and Bernardo Silva slipped Aguero in behind David Luiz with a perfectly-weighted through ball, with the Argentine duly powering a low effort beyond Willy Caballero to double his and his side's tally for the day.
City were good value for their two-goal lead as they regularly threatened a Chelsea side that seemed to have little response to their vim and vigour in attack.