The win, secured thanks to a brace from defender Andrea Dossena, was rendered meaningless by Udinese's 2-0 win over Catania which meant that they finished third, with Walter Mazzarri's side having to settle for fifth place and a place in the Europa League next season.
Mattia Destro scored Siena's consolation as they completed a successful season in 14th place.
All of the action came in the first half with the two sides unable to maintain such a fast pace in the second 45 minutes.
Napoli took the lead in the third minute with Goran Pandev sending Marek Hamsik into the penalty area, and the Slovakian pulled the ball back for Dossena to beat Simone Farelli inside his near post.
The lead lasted just three minutes, though, before Destro levelled.
Morgan de Sanctis made a mess as he came off his line to meet Destro, but he got his timing all wrong, allowing the on-loan Genoa forward to get the better of him and send the ball into the unguarded goal.
Paolo Cannavaro was unable to make a clearance on the goal-line.
Napoli regained the lead in the 34th minute with Christian Maggio sending fellow defender Hugo Campagnaro into the area, and his cross was pushed out to the feet of Dossena by Farelli, and the left wing-back grabbed his second.
Pandev should have made it three before the break, but he sent his shot high into the Naples night sky from Dossena's cross.
Campagnaro then made a goalline clearance to deny Gaetano D'Agostino and keep Napoli in front at the break.
De Sanctis made up for his first-half mistake with a strong second-half performance, making at least three excellent saves to earn Napoli all three points, earning them fifth spot in Serie A and a place in the play-off for the Europa League group stage in August.