A brace from Miralem Pjanic saw Roma equal the best-ever start to a Serie A campaign with their eighth win in a row, although the Bosnian's second came from a highly-contentious penalty awarded against Paolo Cannavaro, as the Partenopei defender was adjudged to have fouled Marco Borriello despite having his own shirt pulled.
Benitez felt aggrieved at the decision and the ensuing red card, as he felt his side were in control of proceedings for the majority of the match.
"The penalty changed everything. Everyone told me it was not a penalty," he told Sky Sport Italia.
"You can see 50 of those tussles in every game. I am not here to say whether it was a penalty or not, as that will be down to the referees to judge.
"I think we had a difficult opening 20 minutes, then for the rest of the first half did very well, in my view better than Roma.
"After the break we controlled everything, but with the penalty it was over. If Roma defend with 11 men behind the ball, it's not easy to find space. We got through anyway and hit the woodwork, so were unlucky."
Napoli striker Gonzalo Higuain started on the bench due to a thigh injury and Benitez denied reports the Argentine had asked not to be in the starting XI.
"I made the decision. We watch the players in every training session and I decided it was better to start with (Goran) Pandev," said the former Liverpool boss.
"If we find space for the rapid counter-attack, then we make it difficult for anyone.
"We had a few chances and moved the ball around well, but against a strong side like Roma to concede a goal on the stroke of half-time and another on a penalty it becomes difficult for everyone.
"I look at the performance and in terms of character, Napoli did very well this evening.
"I said beforehand this game would not decide the title, but clearly with the way we played tonight I'd say it was a positive evening. We played well and this bodes well for the future."