"We're proud of qualifying but there could have been other Italian sides there. Unfortunately there aren't any. It's disappointing," said Milan striker Mario Balotelli.
Juventus only needed a point at Galatasaray but were dumped out in Istanbul on Wednesday, when former Inter Milan midfielder Wesley Sneijder struck in the 85th minute after the match was suspended on Tuesday due to intense snowfall in the Turkish capital.
Both teams struggled on a muddy pitch which made passing a major challenge, forcing them to hit long balls.
"What made me angry was yesterday the referee suspended play because it was dangerous and all of a sudden today it was no longer dangerous.
"Maybe I need to improve my English, as the officials didn't seem to understand me very well."
Napoli were unlucky not to make it through after collecting 12 points in a group that contained last year's finalists Borussia Dortmund and Arsenal, who are five points clear at the top of the Premier League.
They finished on the same points as those two sides after beating Arsenal 2-0 on Wednesday, but were eliminated after Kevin Grosskreutz's weak shot slipped through Marseille goalkeeper Steve Mandanda's fingers three minutes from the end of Dortmund's 2-1 win in the south of France.
It was a tough end to a Champions League campaign that began so promisingly with a thrilling 2-1 home defeat of Dortmund.
"We've beaten the Premier League leaders, I can't believe we're not in the last 16," said a distraught Napoli striker Gonzalo Higuain, who left the San Paolo field in tears.
The defeat was another blow to the prestige of Serie A, which has been overtaken by the top-flight leagues in England, Spain and Germany in the last decade.
Once considered the world's toughest, the league has been dogged by poor management and corruption scandals, and matches regularly play out in front of sparse crowds at dilapidated stadiums.
The weakest of the three Italian teams, Milan are having a deeply mediocre Serie A season and may be the least favoured side in the last 16 of the Champions League.
Antonio Conte's team squandered points early in the group stage as their league form dipped, with poor finishing in Copenhagen and defensive blunders against Galatasaray in Turin costing them two wins that would have sealed qualification.
Elimination will be especially galling to Conte given the impressive displays in his team's recent two matches against Real Madrid.
Poor form in Europe, and in particular in the Europa League, cost Serie A a fourth Champions League spot, and the country's current UEFA coefficient points tally is much closer to fifth-placed Portugal than to Germany in third.
With the Europa League final to be played in the Juventus Stadium, both teams will have to reverse a worrying trend if they hope to see Italian football remain near the top in Europe.