Kevin De Bruyne came back to haunt his former club to score the only goal of the game in West London as Pep Guardiola's side picked up a deserved victory from a match which was a lot more one-sided than the final scoreline suggests.
City had lost top spot to local rivals Manchester United earlier in the day, but the victory takes them back to the summit on goal difference as they recorded an eighth consecutive victory across all competitions and proved their serious title credentials in the process.
Chelsea were able to include Eden Hazard from the start for the first time in the Premier League this season as Antonio Conte made two changes from their impressive midweek win over Atletico Madrid, with Victor Moses and the suspended David Luiz missing out.
City were without their own top scorer Sergio Aguero, and in his absence both De Bruyne and David Silva tried to take on the goalscoring mantle with efforts which failed to unduly trouble Thibaut Courtois.
The visitors were dominating possession without creating chances, but the opening goal almost arrived courtesy of a calamitous error when Courtois took too long on the ball and saw his clearance blocked by Gabriel Jesus inside the six-yard box. The rebound could have gone anywhere, but fortunately for Chelsea it flew off target as Courtois's blushes were spared.
The hosts were struggling to get into their usual rhythm but did test Ederson for the first time shortly before the half-hour mark when Cesar Azpilicueta's snapshot needed to be turned around the post.
City immediately responded with a lightning-quick counter-attack which ended with Raheem Sterling in a promising position inside the area, but his final delivery was too far in front of Silva and Jesus when a better ball would have left either with a tap-in.
Silva came close with a powerful drive shortly afterwards, though, and Nicolas Otamendi also squandered a sight of goal when he got his head to a corner moments later.
A frustrating half for Chelsea got even worse with 10 minutes remaining until the interval when Morata was forced to limp off, and Conte notably selected Willian as his replacement ahead of Wednesday's Champions League hero Michy Batshuayi.
The change did nothing to quell City's dominance of possession, though, and the visitors had their best chance of the first half in the final minute before the interval when Courtois pulled off a fine reaction stop to deny Fernandinho's powerful header.
It was a similar story in the second half as City saw even more of the ball without initially being able to produce the end product, although Sterling should have done better when he volleyed over from the edge of the box despite having time to set himself.
A momentary lapse in defence almost cost City just past the hour mark when Cesc Fabregas's quick free kick released Hazard, whose powerful drive across goal was pushed away by Ederson.
The visitors' pressure began to grow shortly afterwards, though, with Silva and Jesus both coming close in quick succession before the breakthrough finally arrived in some style.
The only thing lacking from City's performance up to that point had been a moment of telling quality in the final third, but De Bruyne provided that by playing a one-two with Jesus before blasting an unstoppable strike past Courtois from outside the area.
Not even the opener could spark Chelsea back into life, and it was City who came closest to adding to the scoring when Antonio Rudiger cleared Jesus's volley off the line with just six minutes remaining.
Chelsea did threaten an undeserved equaliser in the final minute of normal time when Andreas Christensen rose highest in the box, but he could not trouble Ederson with his header and the main concern for City in the closing stages was De Bruyne limping off late on.
The result means that City have now kept four consecutive Premier League clean sheets for the first time under Guardiola - scoring 17 goals without reply in that time - while they have also won their last five top-flight away games, equalling the club record initially set in 1912.
For Chelsea, defeat means that they have now dropped eight points at Stamford Bridge already this season having given up just six throughout the whole of their title-winning campaign last term, while they have failed to score in back-to-back home Premier League games for the first time since November 2012.
Indeed, it is the first time Conte has ever seen one of his sides draw a blank in two consecutive home matches, with the Blues now sitting six points behind the Manchester clubs in fourth place.