The object, which Wenger believed to be a bottle, was launched at the Gunners' boss after Arsenal had secured a 0-0 draw in the first leg at the Ataturk Olympic Stadium.
“As I left the pitch a bottle or something was thrown at me,” said Wenger, who was not hit by the missile. “I reported the incident to UEFA."
European football's governing body will now investigate the episode which came at the end of what proved to be a rather volatile encounter.
Wenger was also upset by the performance of the referee, Milorad Mazic, who sent off Aaron Ramsey for a second bookable offence with 13 minutes remaining. Ramsey, who scored the winner against Crystal Palace at the weekend and was also on the scoresheet in the Community Shield a week previously, will now miss the second leg after being shown a red card for first time in his club career.
A challenge by Besiktas striker Demba Ba which ended Mikel Arteta's night early also prompted ire from Wenger. The Spaniard turned his ankle and left the stadium wearing a protective boot. He is a doubt for the weekend's Premier League clash with his former club Everton.
Arsene Wenger - Arsenal manager
“Neither the first nor the second yellow card was deserved [for Ramsey],” Wenger said.
“When you see some of the fouls made tonight and we go home with Ramsey red-carded, it’s a bit unbelievable. The challenge on Arteta was very bad but the referee was on the pitch and didn’t see anything of it. It’s very difficult to understand but, in the second half, the performance of the referee was very bad.
“We had Ramsey’s second card … it was wrong and it was a huge decision. I felt just a lot was wrong in the second half but, overall, perhaps it was a difficult game maybe to referee as well. Everybody did fight for every ball. Maybe it was not easy for the referee as well.”
Arsenal's Aaron Ramsey trudges off following his red card against Besiktas (AFP)
Meanwhile Wenger's opposite number Slaven Bilic was sent to the stands by the Serbian official following a series of outbursts.
“It was a big game for us, right, and I just wasn’t happy with some of the decisions,” said Bilic. “He just showed me the way [off]. After the game I apologised to him and to Mr Wenger. I made a mistake.
"Maybe I overreacted in that situation when he stopped the game when the ball hit [Mathieu] Flamini in the stomach and we were in a good position, two against one... But nothing serious happened in that moment or after the game."
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