Aguero opened the scoring with a stylish solo effort, jinking his way past three challenges before stabbing the ball over Mohd Farizal Marlias.
The Argentine then turned provider with a perfectly-weighted through ball to Carlos Tevez, who finished well into the bottom corner two minutes into the second half.
Aguero was the architect again for the third with a lofted ball to Adam Johnson, who slotted into the goal, before Azamuddin Akil claimed a consolation for the hosts after Pablo Zabaleta's error.
Roberto Mancini opted for a back three for the second consecutive game, with some predicting that he is testing the new formation in expectation of Daniele De Rossi’s arrival from Roma.
The Italy midfielder has been linked with a move to City, and Mancini clearly feels he can improve on his options in midfield – and experimented with a five-man midfield in Kuala Lumpur.
Abdul Razak, Denis Suarez and the outstanding Yaya Toure occupied central midfield against a Malaysia All-Stars side that pushed Arsenal all the way last week, before eventually succumbing to a 2-1 defeat.
But the hosts were not given a look-in during a game that City utterly dominated.
Aguero, whose partnership with Tevez is improving with every pre-season game, looked particularly sharp - and he could have given City the lead when Yaya’s mazy run and pass found Tevez, who rounded the goalkeeper - Aguero took over but struck the bar with the goal gaping.
But Aguero made no mistake moments later – opening the scoring with a wonderful individual effort.
Receiving the ball on the edge of the box, Aguero skipped away from a first, second and third challenge – before lifting the ball over Farizal with a delectable flick of the outside of his right foot.
Aleksandar Kolarov and Johnson each came close as City threatened to add a second in the first half.
But the travelling City support didn’t have to wait long into the second half for another goal – and Aguero was the architect. The Argentine spotted the run of his compatriot Tevez with a perfectly-weighted through ball – and Tevez slotted inside the far post with a low left-foot finish.
Malaysia barely had time to re-group before it was 3-0 – with Johnson capping a good display with a goal.
Aguero claimed his second assist of the game with a delightful lifted pass over the Malaysia defence to find Johnson, and the England midfielder took a touch before slotting inside the post.
A host of changes ensued as Malaysia engaged in a damage limitation exercise – but it was clear City struggled to create as many chances after the withdrawal of Yaya Toure.
Several youngsters were given a run-out including George Evans, Marcos Lopes and Mancini’s Filippo – but City were unable to see the game out without conceding.
Having kept clean sheets in their previous three games, Mancini must have hoped his new-look back three would remain unbreached – but Zabaleta was caught out and Akil made the most of the space he found, firing a low effort beyond substitute goalkeeper Tobias Holmen Johansen.
The consolation goal flattered the hosts, who were outfought and outclassed throughout, and City look to be getting ever stronger ahead of the first defence of their Premier League title.