Juventus endured a difficult trip to Naples, with their team bus getting pelted with eggs both on Saturday and before the game on Sunday, and they met stern opposition in Benitez's side.
Jose Callejon netted the hosts' first goal in the 37th minute despite appearing to be in an offside position and they generally dominated proceedings until they got their second nine minutes from time.
Substitutes Goran Pandev and Dries Mertens combined and the Belgian winger fired past Gianluigi Buffon to end Juve's 22-match unbeaten run in the Italian league.
Napoli enjoyed a commanding display at Stadio San Paolo but Benitez acknowledged that Juventus made it difficult as they put most of their players behind the ball.
The Spaniard told Sky Sport Italia: "It is not so easy to play with a team that has many players behind the ball, we had a great ball possession in the first half.
"We did very well but we were not perfect because we have failed some things. The key to victory was the possession; it was difficult for Juve to reassemble without retrieving the ball."
Even though Napoli picked up an impressive victory and subsequently ended Juve's excellent run, Benitez was quick to insist that his side were not impressive and he told his players to keep improving in order to reach the defending champions’ level.
"The perfect evening? You can always improve; I saw a great performance against a very good team," Benitez said.
"The squad is competitive, Juve is targeting a championship record but we managed to stop them.
"Now we cannot do anything about the past, it is always difficult to play at a high level with the same intensity after a few days. We need to improve to reach the level of Juventus."
