Arsenal got the job done. It was not pretty and it was a little bit nervous towards the end, when Gonzalo Higuaín, predictably, scored against the club that tried to sign him in the summer and Mikel Arteta, the Arsenal captain, was dismissed for a second yellow card in the 77th minute. José Callejón scored with the tie's final kick.

But Arsène Wenger's team are in the knockout phase of the Champions League for the 14th season in succession and, in truth, their progress was never in doubt. They would have had to lose by three goals at this crackling venue and, despite the late drama, that did not look likely. Callejón's effort made things look tighter for Arsenal than they really were but his was nothing more than a consolation, which was barely celebrated by the Napoli support. For them, it rang hollow.

The sting had come moments earlier and if it represented the death knell for Napoli's Champions League adventure, it was not good news for Arsenal, either. Rafael Benítez and Napoli had needed to better Dortmund's result in Marseille and had looked set to do so but, with two minutes remaining here, the news of Dortmund's winning goal came in, cutting through the tension to bring deflation.

Napoli are out with 12 points; they are this Group of Death's casualty and, according to the club's president, Aurelio Di Laurentiis, there were tears in the dressing room. Yet, for Arsenal, it meant they were pipped to top spot by Dortmund on goal difference and, consequently, they will enter the last-16 draw on Monday among the non-seeds. They will face Real Madrid, Barcelona, Bayern Munich, Atlético Madrid or Paris St-Germain.

It is a sobering prospect and one that sparked the mixed feelings in Wenger and the squad. Here was the opportunity to get the result that, theoretically, stood to make things easier in the next round. It was passed up as Arsenal were caught between ensuring they achieved their basic objective and pushing for the bonus. The defender Per Mertesacker said his team had given "10 per cent less mentally because we knew we were through".

There were echoes of Arsenal's last-16, second-leg tie at Bayern Munich last season, when the Germans had to avoid a 3-0 defeat to progress. Arsenal won 2-0, as Bayern struggled to find the balance between attack and defence. It is never easy but, at least, Arsenal did not come unstuck. It was a curious performance from them, controlled and comfortable for long periods but never truly packing an attacking punch.

They created the best chance of the first half, on 23 minutes, when Mathieu Flamini's lovely first-time touch following a thrusting team move ushered in Olivier Giroud. The striker shot for the far corner only for Rafael, in for the injured Pepe Reina, to save. Mesut Özil addressed the rebound but, under pressure, could not get his shot away.

It was difficult to remember much else from Arsenal and their evening became characterised by the fight to keep Napoli at arm's length. Benítez's team had started brightly, pressing and hustling Arsenal's from their stride, but as Arteta and Flamini exerted their influence, Santi Cazorla delighted in little bursts and Laurent Koscielny showed his composure on the ball, Arsenal gained control.

The only alarm before the interval was sparked by Wojciech Szczesny, who showed flashes of too much comfort. He rushed, ill-advisedly, from his line and was fortunate that Christian Maggio's lob was too high, while an attempted clearance for Koscielny went straight at Higuaín, who, instinctively, directed a header at goal. It went wide.

There had been frustration for hundreds of travelling supporters when the coaches that Arsenal had provided to transport them to the stadium departed late and did not arrive in time for kick-off. The club had wanted to ensure their safety amid fears of further fan violence involving Napoli's ultras. Once inside, they could enjoy the atmosphere but the second half was less pleasurable. Pablo Armero raced on to the substitute Lorenzo Insigne's flick only to shoot at Szczesny; Callejón fizzed a drive past the far post and Higuaín got into dangerous areas. While Dortmund were level in Marseille, Napoli could hope and their evening was ignited when Higuaín took his big chance, with a low and unerring finish. Cue delirium, particularly from the PA announcer.

Gonzalo Higuaín, right, is distraught at the end of the Champions League tie with Arsenal after Napoli fail to go through, despite a 2-0 win. Photograph: Carlo Hermann/AFP/Getty Images

Arsenal did not need to panic, although the wobble became more pronounced when Arteta nibbled at the back of Callejón to incur his second booking. Wenger admitted that "doubt crept in" at what was a "difficult moment." Callejón's fall and roll was theatrical and Arteta will be suspended for the last-16, first leg.

But Arsenal kept their composure and, although Callejón went through to lob Szczesny, the die was cast. The merits of second place remain dubious.