The visitors, with Brian Kidd in charge after the sacking of their manager the night before, see of Nigel Adkins's already-relegated side, doubling their lead late on
The Argentine scored his 17th of the season just before half-time following one of several breathtaking passing moves, with the Bosnian firing home after a great David Silva pass, while the hosts could have been demolished if not for Alex McCarthy's superb display in goal.
Nigel Adkins retained the starting XI from Reading's 4-2 win over Fulham while City caretaker boss Brian Kidd made four changes from the side beaten by Wigan in the FA Cup final, with Micah Richards, Joleon Lescott, Kolo Toure and James Milner replacing Pablo Zabaleta, Matija Nastasic, Vincent Kompany and Samir Nasri.
Milner carved out a terrific chance after just three minutes, skipping past the midfield to lay a crisp pass to Aguero on the right-hand side of the box, the Argentine drawing a fine double save from McCarthy.
McCarthy was called into action again and again, saving from Silva before the onslaught continued and Carlos Tevez set up Milner inside the box, the England international's shot palmed away before Aguero's strike on the rebound was blocked.
The hosts eventually broke into the City half and Hal Robson-Kanu had Joe Hart at full stretch with a great shot from long range.
The Royals were forcing themselves into the contest after a poor start and Garath McCleary drew Hart into another big save, the goalkeeper diving to his left to palm away a right-footed curler.
Tevez should have put City in front after half an hour but the Argentine mishit his shot from Yaya Toure's dinked ball over the top.
Reading posed a large threat on the break and Robson-Kanu again tested Hart, this time with a placed effort from the edge of the box after Jobi McAnuff's lay-off as the action swept from end to end.
Aguero finally put City into a deserved lead after 40 minutes, poking home from 10 yards after a tremendous passage of one-touch passing from a short corner by Milner and Silva. It was almost two for the striker a minute later but, once again, McCarthy pulled off a great save to deny him.
Reading should have been level after five minutes of the second half, Pavel Pogrebnyak heading right at Hart from close range from a tasty right-wing cross. City broke immediately and Tevez glided into the box, perhaps taking a touch too many before his eventual shot was sent over for a corner.
The away side were playing some truly sublime stuff in attack and another slick move saw the ball fall to Yaya Toure, the Ivorian forcing McCarthy into yet another great save.
City were inviting pressure and Reading almost made them pay for their missed chances, Adrian Mariappa with a good header from a cross that Hart picked out.
At the other end, McCarthy's heroism continued, tipping Yaya Toure's rising strike over the bar before Richards's bicycle kick bounced wide of the post.
Mariappa was a bother in the air all evening and he very nearly got an equaliser for his side, heading Danny Guthrie's delivery to the top corner only for Tevez to clear it off the line.
McCarthy had to make further saves from Gael Clichy and Yaya Toure in the final minutes, capping off a phenomenal display, but the goalkeeper was eventually beaten for a second time, substitute Dzeko firing home from Silva's pass.