After the Argentine opened the scoring, the red-hot Raheem Sterling then doubled the advantage, before Harry Wilson struck a sumptuous free-kick into first-half stoppage time to give the Cherries hope, only for Aguero strike shortly after the hour-mark, to see the Pep Guardiola's men eventually ease home on a baked South coast afternoon.
Citizens into early stride
As the Cherries deployed a wing-back system in the attempt to smother the swashbuckling champions, Eddie Howe's decision began to bare early fruit,
Josh King's opening-minute snap-shot already improving on their efforts on target in the two side's last meeting, however at the other end, City quickly hit their stride quickly as Bernardo Silva's cued shot went narrowly wide of Aaron Ramsdale's post from close range.
Bournemouth's ploy of looking for greater width saw both Kyle Walker and Ederson's pick up early cautions - the latter hauling down of Callum Wilson on the touch-line - as the hosts looked to get an improved hold on the game following March's drubbing.
Aguero however, had other ideas and gave the Citizens a 15th-minute lead. Following Oleksandar Zinchenko's galloping surge down the left wing, his cross found Kevin De Bruyne, whose scuffed shot bounced into the Argentine's path to open the scoring.
David Silva then forced a save from Ramsdale to deny a second for Guardiola's men, but the host's concerns were then re-directed to the stricken Charlie Daniels who was forced off with a suspected dislocated kneecap, after stretching to meet a cross.
Harry Wilson was brought on to replace the injured full-back and the change of system somewhat galvanised the Cherries, indeed Adam Smith looked certain to score after Nicolas Otamendi's erroneous knock down for his goalkeeper, forced Ederson into a point blank range stop with the open goal gaping.
The injection of vim in Howe's men then seemed to be short-lived, as Sterling pounced to double City's lead. Silva's delightfully weighted poke through the Bournemouth defence found the red-hot Sterling, who took a touch and clipped the ball over Ramsdale to score his fifth goal of the season.
As the opening period entered a lengthy period of stoppage time however, Bournemouth were given a lifeline. From a free-kick on the edge of the area, It was indeed Harry Wilson, who clipped a sublime, 25 -yard curler into the top right-hand corner and past Ederson, glancing the inside of the post.
Not to be outdone, Aguero had a chance to net his double a minute later but blazed his shot over the bar, to signal the end of a lively opening half in Dorset.
As the second half began to a raucous atmosphere on the South coast, Howe's men went in search of an unlikely leveler, and Callum Wilson almost obliged seven minutes on resumption, as again City's Brazilian stopper made a reflex save close in to his left, to deny the Cherries striker.
With Bournemouth having spurned their opening, the visitors then went straight down the other end and with a ball cut back to De Bruyne on the edge of the opposition area, the Belgian - to the bewilderment of many watching - curled his shot wide of the near post.
City however were not to overawed and after a contentious VAR review rejected after Silva was was felled in the box, minutes later however, the Spaniard was on hand to supply the goods and set up Aguero for his brace.
City's midfield magician exchanged passes with his team-mate and jinked through a baffled host defence, sliding a ball into Aguero to poke home to give City a two-goal advantage.
The third goal for City knocked the stuffing out of the hosts, despite both Dominic Solanke and Jordon Ibe being introduced into the action as the second period wended its way to an inevitable conclusion.
Seconds before the final whistle Solanke could have forced a grandstand finish but was thwarted by the industrious Ederson, as City ran out out comfortable winners.