Needing to win by three goals to definitely go through, it took until the 73rd minute for the Italians to get on the scoresheet, Gonzalo Higuain hitting a shot on the turn from around 18 yards to send the home fans into raptures, before Mikel Arteta saw red for a second bookable offence.
VIEW FROM THE SAN PAOLO
By Julian Bennetts
So, Arsene Wenger, is your glass half-full or half-empty? When the draw was made, second place behind Borussia Dortmund would not have been sneered at, but this was a real opportunity missed. Arsenal were in control in Naples but let it slip, and they paid a heavy price with their potential opponents in the last 16.
They created few opportunities and were punished when Gonzalo Higuain scored, with Jose Callejon's late, late strike counting for little. Ultimately, though, this was a fantastic Champions League group, the first time three sides have finished on 12 points. Napoli were unfortunate and Dortmund lucky, while Arsenal probably got what they deserved for slackness on the final day.
Jose Callejon added a second for Napoli at the death, but it was too little too late for the Serie A club.
Arsenal go through as runners-up and have now qualified from the group stages for 14 consecutive seasons.
Pepe Reina once again missed out for the hosts, but was fit enough for a place among the substitutes, while Aaron Ramsey and Jack Wilshere dropped to the Arsenal bench in favour of Tomas Rosicky and Mathieu Flamini as Arsene Wenger made two alterations to the side that were held 1-1 by Everton on Sunday.
Napoli applied the early pressure, Goran Pandev forcing Wojciech Szczesny into a save from a tight angle in the ninth minute after receiving the ball from a Dries Mertens cross.
Wenger’s men weathered the early storm and Olivier Giroud finally posed a threat at the other end of the pitch in the 23rd minute, with stand-in keeper Rafael Cabral punching away his effort from the left-hand side of the penalty area.
Christian Maggio then found some space down the right seven minutes before the break, but chipped over with Szczesny advancing, before the Pole’s blushes were saved as Higuain nodded wide from a dreadful attempted clearance.
Mesut Ozil unleashed a shot from distance four minutes into the second period, but saw it bounce well wide of the left-hand post.
Pablo Armero was denied by Szczesny at close range, Callejon dragged a shot wide and Higuain blazed over as Napoli reacted to a raucous home support.
But Higuain, who was linked with a move to Arsenal in the close season, appeared to have sent Napoli through in the 74th minute, turning superbly just inside the penalty area and sending a left-footed effort beyond Szczesny for his first goal against English opposition in the Champions League.
And Napoli received a boost just a couple of minutes later, as Arteta was given his marching orders for a second yellow card, before Callejon chipped a second from close range in stoppage time.
But it left the hosts one goal short of qualification as they became the first club to rack up 12 points but not go through to the last 16, while Arsenal could face the likes of Barcelona, Real Madrid and Paris Saint-Germain after finishing second in the group.