Ali has left the Gunners today for Brentford, where he has been named assistant manager to Keith Andrews.
Mertesacker told arsenal.com: "Mehmet has been fantastic both professionally and personally and we are really proud of his development. He has supported both the under-21s and first team amazingly. Since the day Luke Hobbs and I made the decision to appoint him, he has been fabulous.
"We thank Mehmet for his contribution and wish him well with this amazing opportunity to work in a first-team environment and make a difference in the Premier League.
"We place huge emphasis on coach development here at Arsenal and Mehmet has made the most of all the opportunities he has been offered. He has been lifelong learning throughout his time with us and we are so proud of him and wish him well for the future.
“Max Porter and Ken Gillard will take joint interim charge of our under-21s, as we continue to make good progress with our plans for a permanent successor to Mehmet’s role.”