Any hope of the French side progressing disappeared following a fourth straight European defeat in Napoli a fortnight ago, losing 3-2 when the Gunners recorded a superb 1-0 win away at Borussia Dortmund.
Wenger, though, maintains the results to do not tell the whole story for Elie Baup's team.
"They started in a difficult position because they lost their first game at home (to Arsenal)," Wenger said.
"Also they went through a bad patch in the French championship which for me had a consequence on their Champions League form.
"They are a good side who went through a difficult period (domestically) and that difficult period which they had certainly had an impact (on Europe).
"Now, they have played a very good game in Naples and were unlucky to lose.
"I am sure that they will be difficult to beat on Tuesday night."
After losing at home to Dortmund in October, the smash-and-grab raid at the Westfalenstadion secured with a second-half goal from Aaron Ramsey, has put Arsenal back in control of their own European destiny.
Indeed, should Dortmund draw at home with second-placed Napoli and the Gunners beat Marseille, then it would put the Barclays Premier League side through and mean last season's Champions League runners-up would have to be content with dropping down into the Europa League.
Arsenal would then fight it out with Napoli, whom they beat 2-0 at the Emirates Stadium on Matchday Two, to secure top spot and with it seeding for the knockout stage.
Wenger could look to rotate his squad on Tuesday night, with several players have been in action over the international break, when French trio Laurent Koscielny, Bacary Sagna and Olivier Giroud were involved in a dramatic, but draining, World Cup play-off victory over Ukraine.
Arsenal club captain Thomas Vermaelen was, though, glad to get some much-needed match action for Belgium in their friendlies against Columbia and Japan.
The defender, who has seen Per Mertesacker and Koscielny become Wenger's preferred centre-back pairing, intends to remain on full alert to be ready when needed, as he was at Manchester United before the international break when Mertesacker fell ill.
"If I am not ready physically or mentally, I will fool myself because I know that things can change in a split second," he said in the Arsenal official matchday programme.
"I started twice for Belgium during the international break and was really pleased to start gathering some momentum by playing regularly.
"I have played three games in 10 days and it was really important for me to bet back into that rhythm."