Benitez' league leaders made it nine points from a possible nine, although they took until the 71st minute to crack the Atalanta defence through Gonzalo Higuain.
Jose Callejon added a second 10 minutes later much to the pleasure of the Stadio San Paolo faithful.
The former Chelsea and Liverpool manager said he closely monitored the workloads of his returning international stars after the break for World Cup qualifiers and friendlies.
Slovakian midfielder Marek Hamsik was used as a substitute after 66 minutes, while Callejon played just over half an hour.
"I am very satisfied, as we won and also rotated the squad to preserve energy," Benitez told Sky Sport Italia.
"The key to this team is the cohesion of the group. The fans must always stay this close to us, as their support is fundamental.
"We're top of the table, but we should stay calm, as it's still early to judge."
Benitez said Spain international Callejon was particularly important to Napoli's chances of threatening to win their first Serie A title since 1989/90.
"I rotated the squad because some players were tired after international duty," he said.
"Callejon is a very important player for us, because his movements are different to the others we have in the squad.
"In a game like this with limited spaces, he becomes decisive."
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