Marek Hamsik and Jose Callejon came off the bench to rescue the partenopei and inspire them to a third consecutive Serie A victory. Hamsik provided the assist for Gonzalo Higuain to open the scoring. Callejon added a second to make it three goals in as many games for the former Real Madrid player. Ex-Napoli man Luca Cigarini saw red late on for two bookable offences.
Rafa Benitez had the luxury of a full squad at his disposal, but opted to rest several starters ahead of the midweek Champions League opener against Borussia Dortmund. Dries Mertens, Paolo Cannavaro and Blerim Dzemaili were the main beneficiaries of a runout for the home side, who sported their new camouflage kit.
Atalanta missed injured trio Gianpaolo Bellini, Luigi Giorgi and Riccardo Cazzola. Stefano Colantuono handed 21-year-old midfielder Daniele Baselli a surprise start, while German Denis lined up against his former employers.
Atalanta goalkeeper Andrea Consigli flew out to block Dzemaili's early header, before Cigarini was allowed to run at the Napoli defence and fire straight at Pepe Reina. Denis picked up a low cross in the box, but another poor effort was easily gathered by Reina.
Consigli was called into action again on 13 minutes. The custodian pulled off a superb one handed stop to prevent Goran Pandev firing in from Lorenzo Insigne's pull back.
The visitors refused to sit back. Cannavaro was forced into an acrobatic clearance to cut out a dangerous Cristiano Del Grosso cross, as Atalanta started to look dangerous on the counter attack.
Cigarini sent a free-kick down Reina's throat. From the resulting goal kick, Pandev poured forward and flashed wide after opting to ignore strike partner Higuain, who was in space and screaming for the ball.
Denis continued to be a menace for the Napoli defence. On the half hour mark, the striker clashed with Cannavaro to meet a Del Grosso cross and directed his header just wide.
The chances continued at the start of the second half. Insigne took just 45 seconds to test Consigli. A Denis curler forced Reina into a flying save and Higuain volleyed over from ten yards after Insigne showed great poise by controlling the ball and distributing the pass to his teammate on the half volley.
Benitez brought on the big guns as Napoli started to push Atalanta back. The introduction of Hamsik quickly paid dividends, as he helped put Napoli in front just five minutes after coming on. The Slovakian picked up Pablo Armero's pass and forced his way into the box, turning Mario Yepes, before laying off for Higuain to sidefoot the ball into the far corner of the net.
Three minutes after going behind, Atalanta went down to ten men. Cigarini received a second caution for lunging at Callejon. Consigli saved smartly with his feet to deny Higuain a second, then saw Callejon sweep a shot into the side netting. However, Napoli soon put the game beyond the Orobici with a well worked move nine minutes from the end.
Insigne threaded through for Dzemaili to backheel the ball into Callejon's path. The Spaniard made no mistake as he coolly slotted home a left footed shot from inside the area.
Napoli's tails were clearly up. Hamsik curled a left footed effort wide and Consigli caught an audacious chip as the home side ended with a flourish.
Napoli: Reina; Mesto, Albiol, Cannavaro, Armero; Dzemaili, (Radosevic 85) Inler; Pandev, (Hamsik 66) Mertens, (Callejon 59) Insigne, Higuain
Atalanta: Consigli; Stendardo, (Livaja 79) Yepes, Lucchini, Raimondi; Baselli, Cigarini, Carmona, Del Grosso; (Brivio 66) Bonaventura; (Moralez 59) Denis
Goals: Hamsik 71 (N) Callejon 81 (N)