Chelsea were ahead inside two minutes at the Britannia Stadium when Terry met a Fabregas corner with a powerful downward header.
Stoke pushed forward after the break without ever causing fit-again Chelsea keeper Thibaut Courtois many problems and Fabregas sealed victory with a scuffed finish 12 minutes from time.
"These victories mean more than three points, to win and get three points the players need the right spirit and mentality, to win here they must be a really very good team with the capacity to adapt to Stoke's style of play," Chelsea manager Jose Mourinho told the BBC.
Chelsea, who host West Ham United on Friday, have 42 points from 17 games with Manchester City, who visit West Brom the same day, on 39 and Manchester United on 32.
"Now we have to focus on the three matches we still have until the end of this period," Mourinho said of the clash with Sam Allardyce's West Ham, the trip to Southampton on Sunday and another London derby with Tottenham on New Year's Day.
"Playing against Big Sam is a hard job for us, we have to cope with it. The three point lead we have is a little advantage, it is a little pillow we have to protect us -- we go home happy and pleased with what we did."
Stoke beat Chelsea in this fixture last season but the hosts were always up against it after Terry timed his run to perfection and beat Asmir Begovic with a powerful header for his first league goal in over a year.
Mark Hughes's side tried to harry and hustle Chelsea but the superior class of the leaders always shone through.
Courtois, back after a muscular injury, was rarely troubled although the Belgian needed to produce a fine save midway through the first half from Steven N'Zonzi's deflected strike.
Top scorer Diego Costa should have increased Chelsea's lead when Stoke tried and failed to catch him offside, the Spaniard timing his run perfectly -- only to the skew his shot wide.
Fabregas might have been awarded a penalty when he appeared to be clipped by Ryan Shawcross soon after halftime but Stoke escaped.
Charlie Adam drilled wide from edge of box following neat approach play from Stoke but Chelsea soaked up the pressure and made the points safe when Eden Hazard, who needed lengthy treatment in stoppage time, fed Fabregas and the Spaniard beat Begovic.
(Writing by Justin Palmer; editing by Pritha Sarkar)
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