Frank Anguissa and Amir Rrahmani scored Napoli's goals in an eight-minute spell in the first half before Andrea Pinamonti cut the deficit early in the second period.
Fiorentina earlier remained on Napoli's heels after their 1-0 home win over Cagliari in their first league match since midfielder Edoardo Bove's sudden collapse last weekend.
Lazio will face either Inter Milan or Udinese in the quarter-finals.
Napoli coach Antonio Conte criticised the Video Assistant Referee (VAR) for not intervening to reverse a penalty that Inter Milan's Hakan Calhanoglu eventually missed in their 1-1 draw on Sunday.
Antonio Conte's resurgent side wrapped the match up inside the first half, courtesy of an early Romelu Lukaku goal and a sensational strike by Khvicha Kvaratskhelia.
Victor Osimhen has been sidelined by Napoli after the team he fired to Serie A glory just a over year ago left him both off their squad list for the 2024/25 campaign and potentially in season-long limbo.
Belgium striker Lukaku completed a permanent move to Napoli from Chelsea on Thursday, ending a long period of limbo with the Blues.
The futures of Napoli striker Victor Osimhen and England international Ivan Toney are set to dominate the final day of the European transfer window on Friday as Chelsea continue their frenzied pursuit of new signings.
Napoli manager Antonio Conte apologised to the club's fans after his side were humbled 3-0 at Hellas Verona in Serie A on Sunday and said he took responsibility for the loss.
Napoli have insisted that Gonzalo Higuain has not asked to leave and say Juventus have not put in a request to sign him.
Italy veteran Andrea Pirlo is among the absentees as coach Antonio Conte names a provisional 28-man squad on Monday for a pre-Euro 2016 training camp with several stars absent with Cup finals to play.
Gonzalo Higuain hit a hat-trick to set a new all-time record of 36 goals in a single Serie A season as Napoli secured second spot and Champions League football with a dramatic 4-0 rout of 10-man Frosinone.
Dries Mertens treble keeps Maurizio Sarri's men six points behind leaders Juventus
The film will feature never-before-seen footage from Maradona's personal archive and focus heavily on his glory days at Italian soccer club Napoli.
Diego Maradona himself continues to transmit joy, the joy of playing, an art that seems to have been lost a long time ago and has fewer and fewer worthy representatives.
Maradona was chosen number 1 in The Greatest 10 World Cup players of all time by the London-based newspaper The Times. On his 55th birthday, discover the life of Diego Maradona, the footballer as he carved out a special place for himself with his unique talent and skills.
Without many new signings, Real Madrid’s coach Rafa Benitez will pin his hopes on the in-form Cristiano Ronaldo and Gareth Bale for Champion League glory.
Rafael Benitez says he will be leaving Napoli following the final game of the Italian club's season on Sunday.
