European football’s governing body has opened disciplinary proceedings against the Croatia international for “deceiving the referee” in Wednesday’s 3-1 victory over Celtic.
Eduardo went down midway through the first half of the Champions League qualifier despite there appearing to be no contact with Celtic goalkeeper Artur Boruc.
Referee Manuel Mejuto Gonzalez still awarded a penalty, converted by Eduardo who was subsequently condemned by Celtic.
Wenger said: “I find it a complete disgrace and unacceptable. We won’t accept the way we have been treated in this case for two reasons.
“I believe that you can debate whether it was a penalty or not. For me it’s a witch-hunt that we see and not an objective judgement of a case.
“This charge implies there was intent and a desire to cheat the referee. Having watched the pictures again there was nothing conclusive.
“It singles out a player in Europe to be a cheat and that is not acceptable. UEFA has taken action that is not defendable.”
Eduardo could now miss Arsenal‘s opening two games of the Champions League group stage for the incident that even Wenger admitted resulted in a dubious penalty.
But the Frenchman sympathised with Eduardo taking evasive action in light of the career-threatening broken leg he sustained two seasons ago.
And furious Wenger claimed that UEFA would have difficulty proving the 26-year-old intended to deceive the referee.
He said: “We will defend our player as far as we can because he is not being treated fairly.
“It’s funny in football because you can break the legs of players and it doesn’t make a debate for anybody. But this case has been all over the world and Eduardo has been treated like he’s killed someone.
“I’m quite happy that this penalty would have had no outcome on the game. Eduardo has been touched by the goalkeeper and we can prove that.
“I’m the first to say that it doesn’t look like a penalty but it’s another thing to say that he went down with intent. I wish good luck in proving that having seen the pictures again.
“Having seen his leg after that tackle I don’t blame him for getting out of the way of the goalkeeper.”
Scottish FA chief executive Gordon Smith led the calls for the striker to be sanctioned by UEFA amid strong protests from Celtic.
UEFA said in a statement: “Having studied video evidence of the incident in question, the UEFA disciplinary inspector decided to charge the player concerned.
“The UEFA control and disciplinary body will examine the case on September 1.”
In bringing the charge against Eduardo, Wenger insisted UEFA had taken a dangerous route whereby any decision made by an official can be contested after the match.
He said: “There is completely lack of logic in this case. Why? Because people have reacted emotionally.
“This case has been ruled by the media and emotionally by Scotland, by the Scottish FA and by Scottish people working at UEFA who think this case is a bit more sensitive because they have more influence there.
“I’ve fought my whole life against cheating and I’ve seen some obvious cases where UEFA didn’t intervene. On and off the pitch things have happened where no action was taken.
“But now the existing rules of football have been changed just for one case so we will from now on challenge every single decision that is made in Europe by the referees.
“This is the first time since I’ve been in football that the judgement made by the referee is not accepted by the football bodies.
“Usually a situation that has been assessed and judged by the referee can’t be touched again.
“They’ve opened the door to every single decision made by a referee can now on be challenged. They’ve opened a very dangerous door there.”
The timing of the charge is disastrous for unbeaten Arsenal, who now head to Old Trafford for Saturday’s clash with Manchester United mired in controversy.