However, Alex Iwobi and Henrikh Mkhitaryan were named in the starting XI, with Arsenal confirming the playmaker was suffering with a back problem.
Emery stated: "Yesterday he came in with pain and he cannot train yesterday or play today."
The absence of Ozil made little difference, however, as Arsenal claimed a ninth win in a row in all competitions with an emphatic 5-1 success.
But, following that impressive run which has taken Arsenal into the top four and sparked suggestions they could mount a challenge for the title, international football will take centre stage.
Several of Emery's squad will be sent to various corners of the world but the Spaniard is unconcerned that his players could pick up injuries while representing their country.
"Each training also he can [do it]," he added. "For example [we had players playing today who played on Thursday] like Nacho Monreal, Holding, Iwobi and Danny Welbeck.
"I think with preparation they have the capacity to play a lot of matches.
"They are at a big level in the matches and every player wants to play. They’re preparing for that."
Preparation for the clash with Slavisa Jokanovic's side was disrupted by Arsenal's 5,000-mile round trip to face Qarabag in the Europa League in midweek.
Emery took much of his first-team squad to Azerbaijan but was never concerned that his players would be jaded at Fulham.
"No, because I think our players have the habits to play a lot of matches in the week and we want it," Emery explained.
"We arrived very late but Friday we had off to rest the players and Saturday in the morning the first competition for us is speaking about the match today and we worked 24 hours very concentrated to win against Fulham in this match.
"For us and the players in the international break they are going to play Wednesday, Thursday and travel.
"Lucas [Torreira] I think is travelling to Asia, so it’s a very long travel, but the players are at a high level and can play like that."