Emery said Ozil had simply been struggling with illness and he was fit to start the following week against Cardiff.
Arsenal have been handed an injury blow ahead of their trip to St James' Park to face Newcastle on Saturday after Lucas Torreira was injured on global duty.
Here for me it isn't for a lot of the time speaking about what people are telling us.
Emery is hoping for a fresh start for a player he wants to see relishing his opportunity to affect games for the club.
The midfielder was criticised for posing for photographs with Turkish President Recep Tayyip Erdogan in the build-up to the World Cup, which saw 2014 champions Germany knocked out at the group stage.
He said: "First the players have the habits to play in the global break, in important matches, defending their identity and when one player is finishing that, I think it is also good for them to focus only on their team".
Ozil's decision to remove himself from worldwide selection with Germany means he has had time to rest and adapt to Emery's methods.
"I just have a feeling it might work this time".
Ozil has looked slightly out of place when Emery has deployed him on the right wing rather his normal central role as a No. 10, but Emery reiterated that the German is happy switching between the two.
Following talks over the worldwide break, Emery claims the two are getting on and have a good working relationship.
Chief executive Ivan Gazidis' future looks less certain, though, with AC Milan having re-opened negotiations with him.
"Every conversation with him is speaking about us and about our work here every day", he said.