Sampdoria, leading 1-0 thanks to Eder's second-half strike, appeared set for maximum points after Napoli defender Kalidou Koulibaly was given a second yellow card for a trip on the Brazilian forward in the 85th minute.
Napoli then stunned the Luigi Ferraris crowd when Colombian Zapata escaped the attention of four defenders and stooped to head in Faouzi Ghoulam's cross in the second minute of added time.
Sampdoria had taken a deserved lead in the 57th minute when Eder fired a shot inside the near post despite being surrounded by Napoli defenders.
Visiting forward Gonzalo Higuain missed a chance to score for the sixth successive Serie A game when he fired his shot straight at Argentina team mate Sergio Romero following a one-two with Marek Hamsik.
Napoli's point took them up to joint third alongside Genoa on 23 points, one ahead of Sampdoria. Juventus are top with 34 points followed by AS Roma on 31.
(Writing by Brian Homewood, editing by Tony Jimenez)
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