Chelsea were in front with just two minutes on the clock at the Britannia Stadium on Monday night when John Terry rose highest to force home a Cesc Fabregas corner.
Stoke threatened briefly in the second period but Fabregas sealed victory for the visitors with 13 minutes left.
The result means Jose Mourinho’s men pull three points clear of Manchester City.
Stoke had already dished out beatings to Arsenal and Man City this season, but were dealt a major blow inside two minutes as Terry gave Chelsea the lead.
Fabregas whipped a dangerous corner from the right into the danger area and the Chelsea skipper determinedly out-jumped his marker Geoff Cameron to power a header into the net.
Terry has now scored 35 top-flight goals and is Chelsea’s joint 10th top scorer in the history of the Premier League.
The early goal silenced the home crowd as the visitors confidently stroked the ball around midfield, with Eden Hazard causing real problems on the left flank.
Phil Bardsley took matters into his own hands on 20 minutes and received a booking for a wild lunge on Hazard by the touchline that visibly enraged Chelsea boss Mourinho on the sidelines.
The booking seemed to spark the hosts into life and Steven N’Zonzi forced Thibaut Courtois into a save after his 20-yard shot took a deflection.
Diego Costa always looked a threat on the break for Chelsea and he should have doubled the lead on 31 minutes when sent clear by Nemanja Matic, but he dragged his shot wide of the upright.
Substitute Charlie Adam injected plenty of life into the Stoke midfield when he was introduced in the second half and he missed a great chance to level the game on 71 minutes.
Usually so clinical with his left foot, Adam skewed a shot wide of the post from 20 yards after the ball had broken to him very kindly on the edge of the area.
It was a missed chance that proved costly for the hosts as Fabregas wrapped up the points on 77 minutes.
The brilliant Hazard picked out the former Barcelona man with a fine pass inside the area and two touches later, the ball was in the net. It may not have been Fabregas’ most clinical strike, but his rather scuffed effort wrong-footed Asmir Begovic and the ball trickled into the far corner.
Costa should have got his name on the scoresheet when he was released by Andre Schurrle with six minutes left but Begovic did well to deny the striker.
The night was soured slightly for the league leaders when Hazard had to be replaced in injury time by Kurt Zouma after suffering a kick on his heel from Jon Walters, but Chelsea saw the job through with ease.
Chelsea: Courtois (8); Ivanovic (7), Cahill (7), Terry (8), Azpilicueta (7); Mikel (7), Matic (8); Willian (7), Fabregas (7), Hazard (8); Diego Costa (7).
Chelsea subs: Schurrle (6), Drogba (6), Zouma (6).
Stoke: Begovic (6); Bardsley (6), Shawcross (6), Muniesa (6), Pieters (6); Cameron (6), Nzonzi (6); Walters (6), Bojan (7), Arnautovic (6); Crouch (5)
Stoke subs: Diouf (6), Adam (7), Assaidi (6)
Man Of The Match: Matic