Late goals from Thomas Manfredini and Sergio Floccari ended 10-man Napoli's brave resistance and handed Atalanta three vital points in Bergamo.
The visitors fell behind to Ferreira Pinto's 62nd-minute strike and saw their hopes of getting back into the contest diminish when striker Marcelo Zalayeta picked up his second yellow card four minutes later.
Edy Reja's men did conjure a way back into the match, though, with Marek Hamsik converting a 73rd-minute penalty.
It looked as though Hamsik's goal would earn Napoli a point but Manfredini struck with a minute to go before Floccari settled the game with a third for the home side.
Defeat was hard on Napoli, who dominated the first half and battled gamely after the dismissal of Zalayeta, who only entered the fray in the 35th minute as a replacement for the injured German Denis.
Denis looked dangerous early on and it was his third-minute cross which almost resulted in an early opener for Napoli. The center caused panic in the Atalanta penalty area and after Cristian Maggio nodded the ball across the face of goal, home keeper Ferdinando Coppola had to be alert to gather just as Hamsik was about to pounce.
Atalanta responded with a Cristiano Doni shot from the edge of the area which whistled just past the post.
Coppola was dominating his area and he again denied Napoli an opener with a smart take with Denis ready to convert Ivan Lavezzi's pass.
Zalayeta almost made an immediate impact but wasted a wonderful chance six minutes after coming on.
Having been put through by Lavezzi, the Uruguayan tried to lob the advancing Coppola but only succeeded in chipping his effort straight at the keeper.
Atalanta coach Gigi del Neri must have had some strong words with his troops at half-time as they came out a more determined outfit following the break.
And they could have opened the scoring after 48 minutes, Pinto wriggling his way through but failing to find either a shot or pass with Christian Vieri excellently placed to the striker's left.
Experienced striker Vieri did well to hold off his marker 10 minutes later and fire in a shot which Napoli keeper Gennaro Iezzo smothered at the second attempt.
Atalanta's second-half pressure finally told after 62 minutes when Pinto cut inside, beat Matteo Contini and Luigi Vitale before slotting a right-footed shot past Iezzo.
Napoli's woe intensified when Zalayeta departed but the 10 men rallied and found a leveler when Manfredini felled Lavezzi inside the area and Hamsik slotted home the spot-kick.
Manfredini turned from villain to hero with time almost up, lashing home a wonderful 30-yard shot which clipped Walter Gargano on its way past Iezzo.
Napoli heads dropped and they conceded again in injury-time, Floccari converting Pinto's cross from close range.
Napoli stay fourth despite the defeat while Atalanta climb to 10th.
