The Argentine netted a brace prior to his late substitution, while James Milner and Samir Nasri were also on the scoresheet for the champions at the Britannia Stadium
The Argentine marksman had been without a goal in five games across all competitions in 2015 since returning to action after a knee injury - and his fitness concerns resurfaced again at the Britannia Stadium.
|VIEW FROM BRITANNIA STADIUM
|By Tom Maston
Manchester City arrived at Stoke having never won at the Britannia Stadium and in danger of being out of the title race before the resumption of the Champions League, and though they were fortunate at times, this was a clinical showing that showed exactly why they are champions.
They survived an early onslaught from the hosts and were fortunate that in the end the Potters' defence was in even more disarray than their own.
Segio Aguero's opening goal was a sign that the Argentine is getting back towards his best while James Milner underlined his importance to the side with the crucial second goal. Huge question marks still remain, but for now they remain well in the hunt for the title.
James Milner was fortunate to escape punishment for handling Peter Crouch's goalbound header before then setting up Aguero for a superb 33rd-minute opener.
Crouch levelled with his fifth career goal against the Manchester club five minutes later before Aguero was barracked by the home crowd having had a goal disallowed for handball in first-half stoppage time.
But, after Milner had restored Manchester City’s advantage, Aguero netted his 21st goal of the season from the penalty spot.
Samir Nasri scored a brilliant fourth to secure the victory but by that stage Aguero had hobbled out of the action - while a late winner by Willian against Everton at Stamford Bridge preserved Chelsea's advantage.
Eliaquim Mangala and Aleksandar Kolarov were named in a revamped Manchester City defence while Crouch and Milner - included in their respective team's starting line-ups on the back of late weekend equalisers - were involved in an early flashpoint.
Joe Hart turned a stinging sixth-minute effort from Victor Moses behind and Crouch’s header from the resulting corner was blocked in the goalmouth by Milner, with television replays showing Stoke had a strong case in their appeals for handball.
Hart and the Manchester City backline were unconvincing during the opening exchanges and the England goalkeeper was spared by an offside flag in the 20th minute when he spilled Moses’ low cross for Crouch to convert.
A venomous drive from Steven N’Zonzi was parried by Hart and Moses smashed the rebound wide before Aguero took centre stage.
Collecting a long ball forward from Milner, the Argentine grappled with Marc Muniesa on the halfway line and drove purposefully towards the Stoke box before clinically firing into the bottom.
Marko Arnautovic then blasted a shot off target when Hart mishandled again from a corner but the Stoke attacker soon atoned for his error with a superb right-wing cross for Crouch to head home the equaliser.
Aguero then thought he had scored a second on the stroke of half-time, as he converted a David Silva cross from close-range, but he was booked by the referee after handling the ball.
Stoke goalkeeper Asmir Begovic saved with his feet from Kolarov two minutes into a second half that Manuel Pellegrini's team began with far greater conviction.
They were rewarded when Milner planted home a fine 55th-minute header from Nasri's searching right-wing cross to restore the champions' lead.
Moses curled a 68th-minute free-kick off target as Stoke looked to respond but their attacks were increasingly sporadic, and Aguero extended the visitors' advantage from 12 yards after Geoff Cameron had brought down Silva.
Nasri stylishly sealed the points 14 minutes from time, running at a backpeddling Stoke defence to rifle in a 20-yard shot, leaving Manchester City to sweat on their talisman Aguero.