The Gunners were level with the Bundesliga side at half-time, but an onslaught of goals from the Bavarians after the break saw Bayern run away with the match.
Ozil, who had little impact on the game as his team unraveled, came in for criticism for his underwhelming performance but his agent says the negative reactions are far from fair.
"Bayern had 74 percent possession," Dr. Erkut Sogut, who is Ozil's lawyer and representative, said to BBC Sport. "How can someone in the No.10 position create chances if you don't have the ball?
"In these games people usually target a player who cost a lot of money and earns a lot of money - that is Mesut. But he can't be always be the scapegoat. That's not fair."
The agent went on to ask if the attacking midfielder, never really known for his defensive prowess, was the reason the club let the Bundesliga champions score five times.
"Football is a team sport and Arsenal are not performing well as a team. Eleven players were on the pitch but Mesut was singled out for criticism. Was he the reason that Arsenal conceded five goals?
"It started before the match, throughout the week leading up to the game. People started discussing: 'Should he play? Should he be dropped?'.
"It was as if everyone knew Arsenal would not make it through and we needed a scapegoat. This is not right. You win as a team and you lose as a team."
Ozil has often been panned as a big-match flop by his critics, but Sogut was defensive on that subject as well, pointing out several instances where the Germany international came up big for Arsenal while also defending the perception that his client has bad body language.
"I don't agree that Mesut has not had an impact on big matches," Sogut said.
"People are always saying Mesut is not fighting or tackling, that he has poor body language, but that is how he is.
"Believe me, he is desperate to succeed. If it doesn't work, he shows his anger and expressions. Was his body language an issue when Arsenal were playing well?
"He is not someone who runs around aimlessly and tackles just so everyone thinks he is fighting. If it doesn't make sense to run somewhere he will keep that power for the next run."
Ozil and the Gunners will not be back in action until Monday, when they travel to Sutton United in the FA Cup.