Only a late goal from defender Raul Albiol prevented Napoli from suffering a home defeat to the relegation-threatened side, who took the lead after 18 minutes through Gennaro Sardo.
The setback leaves third-placed Napoli 12 points adrift of leaders Juventus and just four ahead of Fiorentina, who can move to within a point of the final Champions League spot with a win over Genoa on Sunday.
And Benitez believes Napoli will not qualify for Europe's premier club competition on current form.
"It is a difficult moment," the Spaniard told Mediaset. "I do not think we are on course to qualify for the next edition of the Champions League.
"We still have to play in the Europa League and the Coppa Italia. We could have done better, but the situation could be worse."
Napoli signed midfielder Jorginho from Verona last week as the Stadio San Paolo club made their first foray into the January transfer window.
And Benitez hinted that Napoli could do further business in the window, but only if the right player became available.
"We continue to work," he added. "We are ready to intervene if we were to find the right reinforcement for us."
