The Gunners needed a point to be sure of seeding for the Champions League knockout stage, but, after their Group F defeat at the Stadio San Paolo coupled with a late winner for Borussia Dortmund in Marseille, they are now set to face one of Europe's leading sides such as Barcelona, Bayern Munich, Real Madrid or Paris Saint-Germain in Monday's draw.
Wenger said: "That is the frustration (not winning the group), because you feel there was room to do better, but it could have been worse as well tonight.
"Of course, to finish second makes the potential draw more difficult. In the last four or five years, we have had very difficult draws, so maybe this time we will be more lucky.
"But if you look at the teams who are potentially there, at least we know we will have a difficult draw.
"On the other hand, we have now qualified (from the initial group stage) for a 14th consecutive year and maybe number 14 will bring us a bit of luck."
Wenger added: "But for now, we have a little breather to focus on the championship. We have a very difficult game on Saturday morning (at Manchester City).
"We will see what comes out of the draw and will assess that in February, because a lot can change on both sides, on us and the team we play against, so we need to put that to the back of our minds now and focus on the championship."
Gonzalo Higuain, who was a summer transfer target for Arsenal, slotted home on 73 minutes to finally break Arsenal's determined resistance and, after midfielder Mikel Arteta was shown a second yellow card, it was always going to be an uphill battle to get back into the tie.
Jose Callejon chipped in a second during stoppage time but it was not enough for Rafael Benitez's men, who must now regroup for the Europa League.
Wenger said: "I felt in the first half we controlled the game well, and, in the second half, Napoli were the better team.
"We prepared well and were concentrated, but we were a bit in between do we attack or do we defend, so it is difficult to cope with that problem.
"In the second half, I felt that our legs went a little bit and Napoli were sharper physically than us.
"They always looked dangerous and won the game 2-0. They deserved it and were always dangerous.
"When we were down to 10 men and 1-0 down, the doubt crept in a bit, and it was a difficult moment.
"But we managed to keep it to 1-0 until the last minute of the game, and it just shows you that this group had three very good teams, who all made 12 points and goal difference played a big part.
"It was always going to be like that when Marseille took no points - one team was unfortunately going to suffer."
Wenger added: "Saturday was on our mind, (but) we knew to come to Naples would be difficult.
"We have done our job now we will give absolutely everything on Saturday morning."
Wenger feels Napoli will be a force in the Europa League, which is a competition Benitez won when in charge at Chelsea last season.
"They have the quality to win it Napoli, but there are some English teams they will have to fight against as well," Wenger said.