Former Liverpool and Chelsea boss Benitez endured a disappointing return to English soil on Tuesday as he suffered a UEFA Champions League setback.
His Napoli side have made a bright start to their domestic efforts this season, but they were found wanting at Emirates Stadium.
Mesut Ozil and Olivier Giroud fired Arsenal into a commanding lead inside the opening 15 minutes, and Benitez admits his Italian outfit were then left with a mountain to climb.
He told Sky Sports: "We made some mistakes.
"We gave them the advantage and we know that they have players with quality, and the first 15 minutes changed the game. It was difficult for us to react and credit to Arsenal because they did well."
Napoli had arrived in north London full of optimism, but saw their pre-match preparations rocked by an untimely injury which ruled star striker, and one time Arsenal target, Gonzalo Higuain out of action.
On the Argentine's absence, Benitez said: "Obviously he is an important player for us.
"When you don't have your main striker then you have to match the situation, and especially when you concede two goals and you know you don't have this option, that makes it more difficult."