Fiorentina were quicker of the two sides in Naples, with Borja Valero trying his luck with long-range shots on two occasions inside the first 10 minutes.
Mounir El Hamdaoui then had two chances to give Viola the lead against Walter Mazzarri's side before Manuel Pasqual tested Morgan De Sanctis.
Napoli created their first chance only in the 33rd minute when Paolo Cannavaro's header from a Marek Hamsik cross narrowly missed the mark.
Fiorentina finished the first half on a stronger note, but conceded just 10 minutes into the second period at Stadio San Paolo when Borja Valero scored an own goal.
The Azzurri doubled their advantage in the 75th minute through Blerim Dzemaili, but Fiorentina halved the deficit with just three minutes left on the clock when Stevan Jovetic found the target.
However, Napoli held on for the final minutes to pick up maximum points in front of their own supporters.