Palermo scored twice in the first half thanks to errors from Napoli with Achraf Lazaar and Franco Vazquez getting on the scoresheet for the home side.
Lazaar's strike from over 40 yards went straight through the hands of Napoli goalkeeper Rafael Cabral, while the visitors gave away possession for Vazquez's goal after two of Benitez's men allowed Robin Quaison to burst away down the left to set up the attack.
"We are punished by our mistakes," Benitez said after the game, according to Napoli's website.
"If we analyse the race you notice that we suffered a goal that no one expected.
"We had possession and control, we had the possibility of a draw, but after a mistake we conceded the second goal. They were our mistakes to influence the game and [I am] sorry after so many good things we have done in these two months."
Napoli could have moved within a point of second-placed Roma with a win at Palermo but instead watched their six-match winning streak in all competitions come to a halt at the Stadio Renzo Barbera.
Cabral's poor goalkeeping kick-started Palermo's victory, which was capped off by Luca Rigoni's 65th-minute goal, but Benitez refused to be too critical of his goalkeeper, who had played in four of the previous six wins.
"He's a guy who has done well and a mistake can happen to anyone. Then the error of the goalkeeper is increasingly evident," the former Liverpool and Inter manager said.
"I have confidence in him as well as I have faith in this team that came from a consecutive series of victories. Now we have to think about the road ahead and we resume our journey."
