Stevan Jovetic scored the first of his two goals even though his strike partner Adrian Mutu was in an offside position when the key pass was fed to him.
Mutu was considered not to be influencing play, whereas under the old rules the assistant would have flagged.
"The new offside rule has changed everything," Benitez told a news conference.
"Now you don't know whether a player is influencing play or not when he's in front of goal. It's very hard for everyone to see when it's offside.
"But I think Jovetic was in a good position. This was a mistake we made."
The five-times European champions have shown some uncharacteristic defensive fragility this season, but Benitez refused to single out his back-line and was confident his men would respond against Chelsea in the Premier League this weekend.
"I was disappointed with the challenges everywhere," he said. "We had too many problems, we made too many mistakes.
"We had to change something and the second half was much better. I think the Chelsea game will be better. We'll see the Liverpool of the second half."
Fiorentina coach Cesare Prandelli was understandably delighted after his side claimed their first points in Group E in style.
"We were very attentive, well ordered and the strikers did very well to be in the right position for the counter attacks," he said.
"The first half was the best performance I've ever seen my team play, given the quality of the opposition."
He also praised in-form Montenegro teen Jovetic, who made sure the suspended Alberto Gilardino was not missed.
"Jovetic has done more than make a leap forward," he said. "Last year his qualities were there for all to see, but it was at the service of his own movements. Now it's for the team".
