Ozil was also criticised for meeting Turkish President Recep Tayyip Erdogan in May, where the pair were photographed holding up an Arsenal shirt, and he has yet to comment on his retirement since he announced it through social media.
The DFB has "emphatically rejected" Ozil's claims of racist treatment and while Gunners manager Emery did not take sides, he offered his support to the German as a member of his squad on a pre-season tour of Singapore.
"We are going to help him feel good and show his quality with us", said Emery.
Erdogan is a controversial figure and his get-together with Ozil and Gundogan came at a time when several German citizens were being held on political charges as part of a crackdown on free speech in Turkey.
Ozil, who signed a new contract with Arsenal back in February, will be aiming to establish himself as one of the key players under Emery next season. "They are great teams with great players, it's a test for us to get ready for the new season so it's something to look forward to".
"In the eyes of Grindel and his supporters, I am German when we win, but I am an immigrant when we lose".
Arsenal news Unai Emery says he wants to help Mesut Ozil return to normality
Speaking ahead of the International Champions Cup match against Atletico Madrid, Emery said: "It's a personal decision (which) I respect".
Ozil also blamed the German Football Federation (DFB) for failing to defend him against his most strident critics. "Here I want to help him and everybody in the club is thinking like me, to help him feel happy and to express his quality with us".
"For us, he's an important player and obviously we're going to support him and make sure he feels right to perform at his best and feels comfortable". They also play Paris St Germain on Sunday.
"I prefer to give him normality in the team, he feels good with us".
"What happened between him and the national team is his private matter so this is not an issue for us", said Cech.
Emery's public support for Ozil was echoed by the 29-year-old's team-mate Petr Cech.