Juventus, crowned Serie A champions on Sunday, won 1-0 at Atalanta in a match interrupted for 10 minutes in the first half as rival fans aimed fireworks at each other.
Inter Milan's accident-prone season continued as midfielder Ricardo Alvarez produced a bizarre penalty miss while goalkeeper Samir Handanovic also blundered in a 3-1 defeat to Lazio at a restless San Siro.
Marek Hamsik, Edinson Cavani, from a penalty and Blerim Dzemaili scored in quick succession early in the second half to guarantee Napoli a second-place finish behind champions Juventus with two games to spare.
They have 75 points, seven more than AC Milan with two games left to play.
Napoli produced a disjointed first-half performance but took the lead eight minutes after the interval when Hamsik turned in Dzemaili's pass.
Ten minutes later, Cavani was hauled down by Bologna goalkeeper Dejan Stojanovic and converted the penalty himself.
Four minutes after that, a powerful run by the Uruguayan ended with the ball running loose to Dzemaili and the Swiss slotted in the third past hapless Austrian teenager Stojanovic, who shipped six goals against Lazio on Sunday.
LEADING SCORER
Serie A leading scorer Cavani took his tally to 27, although it is far from certain he will stay for next season as speculation mounts that one of Europe's wealthiest clubs will cough up the estimated 60 million euro asking price.
Napoli reached the last 16 of the Champions League in 2011/12, when they made their debut in competition.
Juventus rested several first-choice players and an 18th-minute goal from Alessandro Matri gave them their ninth consecutive league win and took them on to 86 points from 36 games, 11 clear of Napoli.
The crowd trouble broke out in the 28th minute and was calmed when Atalanta players went over to appeal to their fans to stop and Juventus coach Antonio Conte did the same for the visiting supporters.
Balotelli hit the bar and converted a penalty in the first 10 minutes to set Milan on the way to an easy win at relegated Pescara, who have taken only two points from their last 17 matches.
Sulley Muntari and Mathieu Flamini scored either side of halftime before Super Mario completed the rout, leaving Milan with 68 points, four ahead of Fiorentina.
UNHAPPY TWIST
An early goal from Gonzalo Rodriguez was enough for Fiorentina in the Tuscany derby at lowly Siena, who protested angrily that the goal should have been disallowed for handball.
Meanwhile, Inter's season, which has seen their team decimated by injuries including a ruptured Achilles tendon for 39-year-old stalwart Javier Zanetti, took another unhappy twist against Lazio.
Their evening began badly when fans displayed banners protesting at the club directors and got worse when keeper Handanovic was credited with an own goal after he fumbled an attempt to punc
