It was a reminder of the old, unreliable Arsenal that a team who started the night top of group F could find themselves contemplating a Champions League knockout round draw on Monday guaranteed an opponent from a group that comprises Real Madrid, Paris Saint-Germain, Bayern Munich, Atletico Madrid and Barcelona.
Yes, Arsene Wenger's team qualified for the 14th season in a row but unfortunately for them they did so as the second-placed team in Group F after Borussia Dortmund's late winner against Marseille. It means that they, like Manchester City, will go into the pot in at Uefa headquarters in Nyon up against the biggest of the big guns in Europe and with their work cut out come February.
By the standards of a season that has gone so well thus far, they took their leave of the Stadio San Paulo like a team who felt the glass was half-empty on a night when they were very close to winning their group. As for poor old Napoli, they exited the Champions League with 12 points and their president Aurelio De Laurentiis called an impromptu press conference to describe the Europa League, in which they will now compete, as “a complete waste of time”.
At least, De Laurentiis reaffirmed his faith in manager Rafa Benitez, the manager who finds himself defending the competition he won as a consolation with Chelsea last season.
In the second half, the pressure on Arsenal became too much to bear and they conceded Gonzalo Higuain's goal and then, with what was almost the last kick of the game, from Jose Callejon. It never looked like the home team would get to the three-goal winning margin required to win the game but even so, given the 12 points that Arsenal have amassed, it feels tough on Wenger's side to face such difficult opposition in the new year.
They had their captain Mikel Arteta sent off for the second of two yellow cards in the second half and were hanging on towards the end. Nevertheless that should not detract from some excellent performances for the away side, especially the central defensive pairing of Per Mertesacker and Laurent Koscielny who relieved a lot of the pressure in the most difficult moments in the first half.
Many of the travelling supporters attending the game found themselves delivered to the ground late in the designated coaches. Whether that was by accident or design on the part of the local authorities was not clear. On the pitch, Wenger's players managed to see off the best of Napoli's early pressure and reached half-time without conceding but they could not hold out in the second half.
It is difficult to know which opponent would represent the best option in the second round. A game in Paris would probably mean the most to Wenger, at a club which has tried to appoint him on a number of occasions. He may also feel that a game against the French champions offers him the best option of a route through to the quarter-finals, in spite of the array of talent their Qatari owners have bought for them.
There was no Aaron Ramsey in the starting XI, given a well-deserved break after that low-key performance against Everton on Sunday. With an early goal for Borussia Dortmund against Marseille, the chase was on for the home team in Naples and their famously committed support were up for it.
Benitez's team looked dangerous in those early stages, with the Colombian left-back Pablo Armero attacking down the wing and the menace of Higuain in attack. Given the scale of the task facing Napoli, it was crucial for Arsenal that they did not offer any encouragement. In those early hectic moments they were composed, with Mertesacker making two crucial interceptions.
In fact, it was notable that in those early stages Wenger's side looked much less fragile than some of its recent predecessors. In the first half, Mathieu Flamini and Arteta were excellent in front of the back four and were it not for two moments of questionable judgement from Wojciech Szczesny then the home side would scarcely have had a sight of Arsenal's goal before the break.
The best chance of the first half fell to Arsenal when they worked a wonderful opening for Olivier Giroud via Mesut Ozil and then Flamini. The French striker's shot was saved well by Rafael Cabral and fell nicely for Ozil just inside the box. Wenger could scarcely hope for a better executioner in such circumstances but the £45m man misjudged, slipped and ended up making a mess of a good chance.
A shot from Callejon from the left wing aside, the momentum was starting to ebb from Napoli as they approached the end of the first half. It was then that Szczesny made his first impulsive intervention, rushing out to the left wing to try to beat Christian Maggio to the ball and losing out.
The Arsenal goalkeeper got away with that one as he did a minute before the break when he tried to chip the ball over Higuain to Koscielny and instead managed only to hit it straight at the Argentine who headed wide. Nevertheless, reaching half-time with the game scoreless was testament to the sensible approach from Wenger's team who had looked well-organised from the start.
It took Napoli time to bring the game to the boil again but around the hour Arsenal faced another intensive period of pressure. Once again, Armero raided down the left and forced an opening. The full-back, however, is so steadfastly one-footed that a shot begging to be hit with his right was struck with his favoured left and saved by Szczesny.
Moments later Kieran Gibbs blocked a shot from Dries Meertens and Arsenal seemed to be coping. The attention in the stand behind the dugouts was briefly captured by two Greenpeace protesters who lowered themselves from the roof of the stadium to unfurl a banner protesting the arrest by the Russian state of an Italian activist. The goal from Higuain on 73 minutes, however, concentrated minds.
The Argentine finally beat Szczesny with a low shot from Callejon's pass. Three minutes later, just after Nacho Monreal had replaced Tomas Rosicky, the Hungarian referee sent off Arteta for his second yellow card. There was contact with his opponent Callejon but nevertheless, the Arsenal midfielder found the decision difficult to accept.
With Dortmund still drawing their game against Marseille at that point, Benitez's team found themselves in a bind. Go for the three goals against the ten men of Arsenal and eliminate their opponents? Or set up to defend the one-goal win and hope that Marseille held out against the Germans?
In the end, the news of Dortmund's winning goal spread around the ground, a wave of frustration. Callejon's late shot past Szczesny barely registered. Benitez's side were out and for Wenger's players, the celebrations on the pitch were muted given the outcome at the top of their group.
Napoli (4-2-3-1): Cabral; Maggio, Fernandez, Albiol, Armero; Dzemaili, Behrami; Callejon, Pandev (Insigne 57), Mertens; Higuain.
Arsenal (4-2-3-1): Szczesny; Jenkinson, Mertesacker, Koscielny, Gibbs; Arteta, Flamini; Rosicky (Monreal 75), Ozil, Cazorla (Ramsey 67); Giroud.
Man of the match Callejon.
Match rating 7/10.
Referee V Kassai (Hun).
Last 16 qualifiers
Manchester United, Real Madrid, Paris Saint-Germain Bayern Munich, Chelsea, Borussia Dortmund, Atletico Madrid, Barcelona.
Bayer Leverkusen, Galatasaray, Olympiakos, Manchester City, Schalke, Arsenal, Zenit St Petersburg, Milan.
Round of 16 draw is on Monday. Teams cannot face anyone from their group or country.
Who English teams can face:
Man City Real Madrid, Paris Saint-Germain, Borussia Dortmund, Atletico Madrid, Barcelona.
Man United Galatasaray, Olympiakos, Schalke, Zenit, Milan.
Arsenal Real Madrid, PSG, Bayern Munich, Atletico Madrid, Barcelona.
Chelsea Bayer Leverkusen, Galatasaray, Olympiakos, Zenit, Milan.