The forward is unavailable due to the fact the striker's former club Borussia Dortmund could still be possible opponents for the Premier League side in the competition.
Wenger upset by Uefa rule that blocks Aubameyang from playing in Europa League
Arsene Wenger has criticised the rule that prevents Arsenal's record signing Pierre-Emerick Aubameyang from facing Swedish side Ostersund in the Europa League on Thursday.
January arrival Aubameyang is unavailable due to the fact the striker's former club Borussia Dortmund could play Arsenal in the Europa League, having dropped into the competition after finishing third in their Uefa Champions League group.
Wenger can call on fellow January recruit Henrikh Mkhitaryan, even though he, like Aubameyang, appeared in the Champions League group stages because his old team Manchester United remain in Europe's premier club competition.
But Wenger, who is also without Alexandre Lacazette after the forward underwent minor knee surgery on Tuesday, believes the Uefa regulation needs changing.
Asked if Aubameyang's absence was caused by an old-fashioned rule, Wenger replied: "Yes. Unanimously, I believe that all the clubs agree now this rule has to disappear in Europe.
"Especially because, for example, he played (for) Dortmund, Dortmund has been reversed in the Europa League and he cannot play.
"When you look at the transfer amounts you spend now, that you have to spend £50, 60, 70million in the middle of the season, that the players cannot play doesn't make sense. Unanimously everywhere in Europe now the clubs are against this rule."
Without Aubameyang and Lacazette, Wenger has confirmed that Danny Welbeck will start along with Mesut Ozil in the first leg.
Ostersund only came into existence a month after Wenger took the reins at Arsenal in 1996 and will present a unique challenge given they play in harsh conditions on an artificial pitch at the Jamtkraft Arena.
Although clubs in European competitions have the option to train at their opponents' ground on the eve of the fixture, the Gunners have opted to remain at their own London Colney base.
And Wenger stressed he did not feel the need to alter those plans for the first leg of this tie.
"No because it is really disturbing the organisation and the way we want to prepare for a game and I think we will adapt," he added.
"We have played sometimes indoors. We have an artificial pitch, even if it is completely different.
"I have heard this is 4G, we have 3G, so it is different and outside it is different as well but no matter we have not to make too big a problem with it."
Ostersund's manager is Englishman Graham Potter, who has led the club from the Swedish fourth tier to the top flight, while they won their first major trophy last April.
Potter's team have already beaten Galatasaray and Hertha Berlin in the competition and their manager has compared Arsenal's visit to an FA Cup contest.
"In some ways I know where you are coming from in terms of the small team against the big team, absolutely," Potter said.
"For us in this type of game, as we have approached all the games in Europe, we have tried to play as well as we can, be ourselves in the game and use the opportunity to show what we are about.
"Normally in the third round of the FA Cup you have not beaten Galatasaray or PAOK or Hertha Berlin. But in terms of the size of the two teams, absolutely. We are obviously all excited about the game and the visit of Arsenal, a Champions League club."