UEFA said on Friday it was opening disciplinary proceedings against Eduardo for "deceiving the referee" after the Brazilian-born Croatian international won a penalty in Arsenal's Champions League playoff victory over Celtic.
"I find it a complete disgrace," Wenger said at a news conference when asked about the UEFA charge.
"There is nothing conclusive (in the pictures). It singles out a player in Europe to be a cheat and that is not acceptable."
He added: "For me it's a witch hunt. It is not an objective judgement of the case. Eduardo was touched by the goalkeeper and we can prove that."
"It is 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 is being treated like Eduardo has killed somebody," Wenger said.
"The existing rules of football have been changed just for this case, so from now on, we will challenge every single decision, I tell you, that is made in Europe by the referees," Wenger said.
"This is the first time I have been in football that the judgement of the referee has not been accepted... So they have opened a door that a decision seen by the referee and assessed by the referee can be challenged. They have opened a very dangerous door there."
