Argentinian striker Denis punishes lifeless Napoli
Atalanta's Argentinian forward Denis German Gustavo celebrates after scoring a goal during the Italian Serie A football match between Atalanta and SSC Napoli at the Azzurri D'Italia Stadium in Bergamo on February 2, 2014 - by Giuseppe Cacace
Three days ahead of their Italian Cup semi-final first leg away to Roma, Benitez chose to rest Gonzalo Higuain, Marek Hamsik and Jorginho despite the prospect of a tricky encounter in rain-hit Bergamo.
Napoli had won only two of their last 10 encounters away to Atalanta and after a stale first half were playing catch-up two minutes after the restart when Denis beat Pepe Reina from distance with a bouncing drive.
Sensing the danger, Benitez sent Higuain on in place of Esteban Zapata on the hour, but barely five minutes later Atalanta doubled their advantage.
Napoli's defence was to blame for the South American's second on 64 minutes, Denis pouncing on Gokhan Inler's poor clearance and taking two touches before beating Reina from just inside the area.
Atalanta virtually wrapped up the points on 70 minutes when Maxi Moralez ran on to Denis's header to beat Reina from close range.
Benitez immediately replaced Blerim Dzemaili with Jorginho then handed new signing Faouzi Ghoulam his debut when the Algerian replaced defender Anthony Reveillere six minutes later.
But the late changes did little to spark a Napoli side which, having drawn with Bologna and Chievo in their last two league encounters, ultimately lacked punch and imagination.
Napoli's first defeat since November has left them in third place but they will see their 12-point deficit to leaders Juventus grow to 15 points if the champions account for Inter in Turin in Sunday's late game.
Roma, in second place at six points behind Juve and six ahead of Napoli, hosted Parma at the Olympic Stadium but their encounter was rained off after just eight minutes after players complained of the impossible playing conditions.
Elsewhere, Sergio Almiron scored a late equaliser for basement side Catania in a pulsating game as they fought back to level 3-3 with fellow strugglers Livorno.
Antonio Candreva and Keita Balde scored one apiece for Lazio in a precious 2-0 win away to Chievo which leaves the Verona-based side hovering dangerously above the relegation zone.
City rivals Verona, meanwhile, moved back up among the Europa League places to fifth after a 2-1 win away to relegation candidates Sassuolo.
Verona were handed a boost when Sassuolo defender Thomas Manfredini turned into his own net on 50 minutes and striker Luca Toni doubled the visitors' lead two minutes from time.
Sassuolo scored a late consolation when Antonio Floro Flores headed past Rafael in the Verona net although his injury-time goal was clearly offside.