The Frenchman, along with midfielder Samir Nasri, have been accused of using "improper language" towards the official following the final whistle after Robin van Persie was controversially sent off in the second half of the game at the Camp Nou.
Wenger told reporters: "I deny completely any charge. I do not understand where it comes from.
"It is a shame for me that the referee took the decision to send Robin van Persie off. It was the wrong decision.
"The first leg was a fantastic advert for football and the second game has been destroyed. People now will only remember the sending off.
"It would be good for Uefa to show some humility, to apologise for what has happened, not charge people who have done nothing wrong."
Wenger was incensed by the second yellow awarded to Van Persie for kicking the ball away barely a second after the referee had blown for an offside, and again expressed his frustration with the official.
He continued: "We are out of the Champions League, we have lost one of our big ambitions, we have been punished with a lot of damages and on top of that we have to say sorry to Uefa.
"We have done nothing wrong. They organised the competition, they named the referees who come to the games.
"When you have a football game of that stature, you cannot come out with decisions like that and show a lot of arrogance on top of that.
"We can all understand that we can make wrong decisions, but after that it becomes dictatorship. It's not any more common sense."
Wenger was asked whether he had sworn at Busacca, which Uefa deemed the reason behind his charge of improper conduct, and gave a cryptic response.
He replied: "I will keep that for Uefa if they really want to know because I will have some interesting statements to make about some statements made by people who were not supposed to say what they said.
"Did Busacca say something back to me? I don't want to go public on that.
"Our not having a shot on target was our biggest problem but that would not have happened had we stayed 11 versus 11, believe me.
"We had already given a lot and to be down to 10 men – the referee knew exactly at that moment in time and I knew exactly what would happen, that in the last 20 minutes, it will be too difficult."