It gave Napoli, who started their third match of the campaign top on goal difference, the chance to pull clear of four other teams who had taken maximum points from their first two games of the season.
And despite Atalanta enjoying the lion’s share of the scoring chances in the first half at the San Paolo, Higuain sent the Partenopei on their way to victory with a well-taken individual effort in the 71st minute.
Atalanta were reduced to ten men a minute later when former Napoli player Luca Cigarini was shown a second yellow card for a brutal tackle on Callejon.
Barely ten minutes later, Spanish striker Callejon finished off good work by Lorenzo Insigne to virtually secure the points for the Neapolitans.
Napoli, runners-up last season, now lead Inter and third-placed Juventus by two points ahead of the rest of the programme on Sunday, when Fiorentina would have to enjoy a goals-fest against Cagliari if they were to dislodge Benitez’s men.
Roma, the only other team to win their opening two games, are not in action until Monday when they visit Parma.
In Saturday’s other late game AC Milan, who suffered defeat in their opening game of the campaign away at promoted Verona, looked to be heading for another 2-0 reverse until a dramatic, late fightback.
Danilo D’Ambrosio gave Torino the lead at the Stadio Olimpico after beating Christian Abbiati in the Milan net following some fine individual skill.
Alessio Cerci doubled the lead when he outpaced the Milan defence on the left flank before beating Abbiati in the 71st minute.
Milan, however, began a most unlikely comeback in the 87th minute when Sulley Muntari’s low shot sneaked into the Torino goal as confusion reigned in the home end.
In injury time, the Rossoneri were handed a lifeline when the referee pointed to the spot after Giovanni Pasquale’s late foul on Andrea Poli in the box.
Although Milan coach Massimiliano Allegri could not watch, Balotelli soothed fears when he stepped up and beat Daniele Padelli at the goalkeeper’s right-hand post to secure a share of the points.
Earlier Saturday, Inter overcame a shaky first half against Juve to grab a 73rd-minute lead through Mauro Icardi, two minutes after the Argentinian substitute had entered the fray.
However, the Nerazzurri’s bid to go top was halted in spectacular fashion when Arturo Vidal levelled only two minutes later and the hosts were lucky to escape with a share of the points as Juve missed three clear chances late in the match.