Supercoppa Italiana champions Napoli had the chance to rise to third in the standings but instead lost against Juventus at the San Paolo for the first time since 2000 following second-half goals to Martin Caceres and Arturo Vidal.
Napoli defender Miguel Britos had cancelled out Paul Pogba's 29th-minute volley after the half-time interval.
The loss angered Spanish boss Benitez, who was less than impressed by the standard of officiating throughout in Naples.
"We all know Juve are a very strong side, that is beyond doubt," Benitez said.
"They taught me a phrase when facing Juventus: 'It can happen.' On the offside it is very difficult to tell, as [Christian] Maggio is right behind Caceres, so it is very tough. It can happen.
"I say when the team recovered its intensity and got back into the game, we conceded that goal. It can happen.
"I 100 per cent believe the decisions were in good faith. [Giorgio] Chiellini is offside and jumps, so he is interfering with play. Last season it was 15cm, this time it was millimetres.
"The [Kalidou] Koulibaly goal that was disallowed – it can happen. Koulibaly jumped, the goalkeeper fell into him, it was [Gianluigi] Buffon's momentum that took him towards the defender. It is not a foul."
Benitez added: "Juve are a very strong side and can win the Scudetto, but we are allowed to complain. Anyway, I don't want to talk about refereeing decisions, especially after losing 3-1.
"I have the right to be angry at the way the game went, we can make all the comments and analysis we want, but in the end we still lost.
"There was another incident too, when Buffon picked up a back-pass from Chiellini. When the team works so hard, I don't enjoy losing like this."
