Having dropped points at West Brom in their last top-flight fixture, Jose Mourinho's men looked set to be frustrated again by an Everton side that had presentable chances of their own.
However, a free-kick from Frank Lampard - who is now up to joint-second on the all-time Premier League appearance list - found its way into the net late on as fit-again Terry applied pressure to Everton goalkeeper Tim Howard.
The goal sent Chelsea four points clear at the summit ahead of Saturday's other fixtures.
Everton, whose last league win at Chelsea came in 1994, remain sixth but have now suffered three successive away defeats to teams above them.
Leon Osman came closest to scoring in a first half short on goalmouth action, forcing Petr Cech into a sharp save from distance.
Both goalkeepers were required to make impressive stops after the interval, before Lampard had the final say.
Terry returned after missing three matches with a muscle strain, replacing David Luiz in Chelsea's defence, while Lampard and Oscar were also recalled.
Steven Naismith - scorer of the only goal in September's return fixture - was drafted into Everton's side at short notice when Lacina Traore picked up a hamstring injury in the warm-up.
Willian dragged a low shot wide as the hosts started brightly, but Everton soon settled, enjoying prolonged spells of possession, and almost moved ahead in the 12th minute.
Naismith laid the ball into Osman's path 25 yards out and the midfielder's powerful first-time shot forced a fine one-handed save from Cech.
Chelsea gradually improved prior to the interval and visiting keeper Howard needed to be alert to deny Samuel Eto'o after the forward had made space for himself inside the penalty area.
Everton's Kevin Mirallas then wasted a fine opportunity just before half-time, scuffing a shot into Naismith having been given space on the edge of the box.
Chelsea, with Ramires on for Oscar, came out for the second period with renewed purpose and Lampard tested Howard following a neat pass from Eden Hazard.
Yet Everton refused to lie down and Osman brought another good save from Cech on 58 minutes with a deflected strike that the keeper did well to parry past his left-hand post.
Not to be surpassed, Howard got down to deny Hazard before springing to his feet to keep out Branislav Ivanovic's close-range follow-up.
Ramires almost broke the deadlock in the 89th minute with a fizzing 25-yarder that flew narrowly wide, but it mattered little as Chelsea secured a precious winner.
