Although it was Torres' first league goal of the season, it was the Spain striker's third this week after also scoring twice at Schalke in the Champions League on Tuesday.
And it ensured that two of Sunday's goals were scored by former Atletico Madrid strikers - Torres and Aguero - in a meeting of one-time Real Madrid managers: Chelsea's Jose Mourinho and City's Manuel Pellegrini.
The early danger was all created by Mourinho's players.
Gary Cahill volleyed over after just three minutes, but both sides were struggling to get sight of goal.
Torres threw his body at Ramires' deep ball after 28 minutes but was unable to get a shot in.
Ramires tried to set up Torres again a minute later, but the end product was poor. Torres brought the ball down with his chest but scooped over with no defenders around him and only Hart to beat.
Still, Torres was looking a real threat, and was the creator of Chelsea's opener.
The City defense couldn't cope with the Spain's striker's blistering pace as he rampaged down the right flank before squaring to Schuerrle, who swept the ball in from close range in the 33rd minute.
Torres was popping up everywhere, and was only denied a goal by the crossbar in the 37th when he unleashed a shot on the turn from inside the penalty area.
In a first half when Petr Cech had little to do, the Chelsea goalkeeper had no trouble batting away a close-range shot from Aguero.
But the Argentina striker was on target four minutes into the second half. He ran onto Samir Nasri's throughball and got past Cahill before beating Cech at his near post.
City kept up the pressure and Javi Garcia met David Silva's free kick with a header that Cech saved.
When Eden Hazard went down in the penalty area under a challenge from City defender Pablo Zabaleta, Chelsea appealed for a penalty that wasn't given.
Torres continued to search for his first league goal since May, but he flicked a header straight at Hart and lifted the ball over at the back post from Frank Lampard's free kick.
Cech's feet prevented Silva from giving City the lead, and Torres then produced the winner with the game about to enter stoppage time - causing Mourinho to launch himself into the crowd behind the bench to celebrate with the delirious Chelsea fans.
It was Chelsea's third straight win, while City has now dropped 11 points in nine games.
The only consolation for City is that they remain two points ahead of reigning champion and neighbour Manchester United.
Other scores:
Sunderland 2 Newcastle 1
Swansea 0 West Ham 0
Tottenham 1 Crystal Palace 0
- AP
