Victory would have taken Jose Mourinho's side above leaders Arsenal, who host Liverpool later today, but instead they fell to second-half goals by Yoan Gouffran and Loic Remy on a rain-soaked afternoon in northeast England.
It was Chelsea's second defeat of the campaign and their second consecutive loss away to Newcastle, while Mourinho has now gone four league games without victory at St James' Park in his two spells as Chelsea coach.
Chelsea's best chances of the first half both came from corners and fell to John Terry, who saw one header come back off the crossbar and another headed off the line by a stooping Davide Santon.
The visitors were happy to cede possession to their hosts, but although Newcastle struggled to create chances in the first half, they began to make inroads in the second period.
Chelsea goalkeeper Petr Cech was called upon three times in five minutes to keep Newcastle at bay, thwarting Moussa Sissoko, Remy and Gouffran in quick succession as Alan Pardew's men took the upper hand.
Mourinho reacted by sending on Willian for Juan Mata, only for Newcastle to open the scoring in the 68th minute when Gouffran converted Yohan Cabaye's free-kick with a diving header.
Mourinho introduced Andre Schuerrle and Samuel Eto'o, and the Cameroonian felt he should have been awarded a penalty soon after coming on when his goal-bound half-volley struck the arm of Mapou Yanga-Mbiwa.
Nothing was given though, and after Willian, Eto'o, Schuerrle and Eden Hazard all went close to an equaliser, Remy swept home a neat cut-back from Vurnon Anita in the 89th minute to seal Chelsea's fate.
Chelsea's defeat saw them slip to third place, with Liverpool overtaking them on goal difference, while Newcastle climb to ninth.
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