The 24-year-old Argentina international opened the scoring with a fine first-half solo effort before setting up strike-partner Carlos Tevez and then winger Adam Johnson to cement the win after the break.
It took Aguero just 17 minutes to make his mark at the Bukit Jalil National Stadium in Kuala Lumpur when, having earlier hit the crossbar and forced a save from goalkeeper Farizal Marlias, he opened the scoring.
The former Atletico Madrid frontman surged past three defenders before chipping a deft shot past Marlias to put the visitors ahead.
Johnson and Tevez both went close before half-time and although Norshahrul Talaha headed wide for the Malaysians in injury time, City went in at the break 1-0 to the good.
However, the game was effectively over within seven minutes of the restart when Aguero fed Tevez to make it 2-0 from a tight angle and then obliged once again to allow Johnson to add a third from 12 yards.
Manager Roberto Mancini made a series of changes as time ran down, Aguero making way for Marcos Lopes with 20 minutes remaining, and the home side claimed an 87th-minute consolation when substitute Azammuddin bin Mohd Akil reduced the deficit.