Jose Mourinho's side headed to the north east on the back of a nine-game unbeaten run in all competitions, but were undone by goals from Yoan Gouffran and Loic Remy.
Chelsea had made the brighter start to the game and struck the crossbar twice in the 13th minute through captain John Terry and fellow defender Branislav Ivanovic following a Juan Mata corner.
Terry saw another header cleared off the line by Davide Santon, while Newcastle could only muster shots from Yohan Cabaye and Moussa Sissoko which drew comfortable saves from Petr Cech.
But Newcastle were much improved after half-time and, after Cech had saved from Sissoko and Gouffran, the hosts took the lead on 68 minutes.
Cabaye curled in a brilliant free-kick from deep and Gouffran had been left unmarked to head beyond an exposed Cech.
The visitors came close to equalising 10 minutes from time when Willian's shot was pushed out by Tim Krul and fellow substitute Samuel Eto'o's follow-up was blocked by Mathieu Debuchy.
Newcastle then wrapped up the points a minute from time when Vurnon Anita's low pass teed up Remy to flash a left-footed shot in off the post to leave Mourinho still waiting for his first Premier League win at St James' Park.
On a miserably cold and wet Tyneside afternoon, the fare on offer initially did little to lift the mood as an attritional game unfolded.
Chelsea started confidently and pinned their hosts back for long periods with Eden Hazard leading the home defence a merry dance.
The inability of Alan Pardew's men to retain possession for anything other than a few seconds left them constantly under pressure with Hazard and Oscar capitalising on their profligacy.
They had to ride their luck at times with the crossbar coming to Krul's rescue twice within seconds in the 13th minute, when Terry climbed highest to head Mata's corner against the woodwork before Ivanovic's deflected follow-up was repelled in similar fashion.
But, for all their pressure, the visitors were unable to test Krul further and, as they gradually found their feet, the Magpies began to compete.
And, as they grew in confidence, both Cabaye and Sissoko tested Cech after more enterprising build-up play.
Newcastle resumed on the front foot after half-time and attempted to attack Chelsea, although their wastefulness in possession continued to court disaster.
But it was the Magpies who went close to the opening goal twice within seconds when Cech made a fine save from Sissoko's skidding 60th-minute effort after he had been played in by Debuchy and Remy volleyed straight at the keeper from Ameobi's knock-down.
Buoyed by the growing momentum, Pardew sent on Papiss Cisse for Ameobi as Willian and Eto'o replaced Oscar and Fernando Torres, but it was Gouffran who tested Cech at the foot of his near post after cutting inside Ivanovic with 25 minutes remaining.
But the Frenchman was not to be denied and he got his reward three minutes later in spectacular style.
Cabaye's curling free-kick caused all kinds of problems for the Chelsea defence and Gouffran read it perfectly to dive and power a header past Cech.
Mourinho swiftly replaced Frank Lampard with Andre Schurrle, but the home side might have increased their lead with 72 minutes gone when Sissoko and Remy carved a path through the blue shirts before the latter saw his shot blocked by the sliding Terry.
However, Krul had to be at his best 10 minutes from time to beat away Willian's snapshot with an instinctive save, and Debuchy was on hand to block Eto'o's follow-up to ensure the points remained on Tyneside.
Hazard fired inches wide with four minutes remaining, but Remy made sure at the death when he thumped Anita's pull-back past the helpless Cech.