Ozil has been left out of both the Europa League and Premier League squads by Arsenal as his contract runs down.
Gundogan and Ozil caused controversy when pictured with Turkish president Recep Tayyip Erdogan before the 2018 World Cup. With his commitment to Germany questioned, Ozil eventually announced his retirement from international football in July that year.
Gundogan has managed to fight on, but Ozil is now in the football wilderness, with little prospect of first team football should he remain with the Gunners to the end of this season. The midfielder's contract expires in June.
Gundogan told RTL via TMW: “Although Mesut is a friend, I prefer not to comment on this situation. I can only imagine how hard this moment is for him, although I am convinced that he will be able to make the most of this situation as well.
“Clearly it's a pity, for him, for Arsenal and for all of German football."
Gundogan acknowledges Ozil's situation hasn't been caused by one single event, but by a series of decisions.
"I believe that this situation has depended on a whole series of circumstances and not on a single position," he added.
Ozil has been with Arsenal since 2013, playing over 180 games. He also retired from the Germany national team on 92 caps.
- updated November 2