The first period at Stamford Bridge was quite a spectacle with good opportunities from Pedro, Diego Costa, Ruben Loftus-Cheek, Kevin De Bruyne and Samir Nasri before Aguero gave City the lead just after half-hour mark.
The result was sealed eight minutes after the restart when Aguero added his second and completed his hat-trick ten minutes from end from the penalty spot after Thibaut Courtois was dismissed to cap off a miserable afternoon at Stamford Bridge.
Many would have expected this match to be a title-deciding contest when the fixtures were announced but this hasn't been the case this season but both sides came out the traps looking like they had everything to play for.
It only took three minutes for midweek hero De Bruyne to link up with Aguero as he pulled it back for the Argentine in the area but Gary Cahill did well to smother the danger.
Guus Hiddink's side had a great opportunity to take the lead just two minutes later when a error allowed Radamel Falcao to go through on goal.
The opportunity didn't open up for him but he did tee up Pedro whose effort had Joe Hart beaten but a touch from the keeper made it easier for Nicolas Otamendi to clear off the line.
Costa had the ball in the net on his return to the side after he coolly finished beyond Hart after Eliaquim Mangala was dispossessed but the Stamford Bridge celebrations were cut short with the flag for offside been raised.
Loftus-Cheek had a good opportunity just before the 20-minute mark when he turned Otamendi and tried to bury his effort into the far corner but Hart did well to see it away from goal.
Courtois sat out of last week's 1-0 defeat to Swansea City and the Belgian went a long way to securing the number one jersey with two great saves in quick succession.
The first came in the 23rd minute when a break from City saw Yaya Toure play a through ball for De Bruyne who did well to get the shot off despite pressure but Courtois did well to save it.
The second followed three minutes later when Aguero put Nasri in on goal but Courtois came flying off his line to close the angle and eventually prevent the danger.
Despite his efforts, Courtois could do nothing to prevent Manuel Pellegrini's side taking the lead in the 32nd minute.
Again it was good build-up play between Aguero and De Bruyne as they broke up field and it was De Bruyne who played it back into the striker. The ball forced Aguero to readjust his body but made no mistake as a slight deflection off the foot of Cahill took into the bottom corner.
They were at it again just before the break as Aguero was put through on goal once again but Cahill did brilliantly sliding in to prevent Aguero possibly completing his brace.
Lightning strikes twice
City had proven difficult to handle on the counter-attack and showed how deadly they can be when they doubled their lead eight minutes after the restart.
There were minor calls for a penalty after Costa was brought down in the area but City took advantage as the visitors broke up field spearheaded by De Bruyne.
The Belgian had been causing his former employers a headache all afternoon and he was at it again with the ball to Nasri who waited to pass to Aguero as he got himself back on side and made no mistake as he placed in the far corner.
A miserable afternoon for Hiddink's side was capped off 13 minutes from the end when Courtois marred his terrific performance with a dismissal. City broke once again this time through Fernandinho who got beyond Cahill and looked to have got beyond the Belgian but he brought down the Brazilian and Mike Dean had no choice but to give him his marching orders.
Aguero had been misfiring from the spot of late with the miss against Paris Saint-Germain midweek been the latest mishap but he made no mistake this time as he put his set piece into the side-netting to round off a great individual performance.
The home side looked for some sort of consolation through Cesc Fabregas but his whimpering effort which was easy for Hart summed up Chelsea's afternoon.