Ozil is expected to finalise terms with the Super Lig giants in the coming days after being given permission to fly to Turkey on Sunday.
The former Germany international struggled to win over Arteta, with his most recent appearance for the Gunners coming last March.
Despite his reluctance to use Ozil, however, Arteta insists that Arsenal will be losing an important player.
"Mesut is in Turkey going through the medical that has to be completed," he told Sky Sports News.
"There is still some paperwork that has to be done but it doesn't matter - Mesut's quality will be missed.
"He's a very special player who has a big history in this football club and if he ends up doing the deal when it happens I will give my clear opinion on that."
Ozil has been with Arsenal since September 2013 and has made over 250 appearances in all competitions for the North London side.