Gunners manager Arsene Wenger said the 28-year-old is expected to be fit for the FA Cup quarter-final tie against Lincoln City on Saturday.
“I don’t think he’s ready to be in the squad,” said Wenger, although Ozil did take part in Monday’s training session.
The French boss has yet to decide if forward Alexis Sanchez will start.
The club’s top scorer this season, with 20 goals, was only a substitute during the 3-1 defeat at Liverpool at the weekend.
The 28-year-old Chile forward had an angry exchange with Arsenal team-mates after leaving training mid-session in the build-up to Saturday’s defeat, although on Monday Wenger denied there had been a row.
Club captain Per Mertesacker could be involved in his first game of the season having recovered from a serious knee injury he suffered in the summer.
The former Werder Bremen defender watched his side concede four second-half goals at the Allianz Arena, having gone into the break level at 1-1 with the Bundesliga champions.
“I want that we are up for a fight on Tuesday, to challenge something,” said the 32-year-old.
“We haven’t competed a lot in recent games, we need to turn that around.
“I think it’s up to us to show a different face. That is really something we are going to demand because we literally blew it away in the second half there and being in that position.
“So it’s really down to us now to make the first step to make our fans proud of ourselves again. That is really something that we need the emphasis on.”
Bayern defender Jerome Boateng is not yet match-fit having been out since November with a chest injury, and defensive player Philipp Lahm is suspended.
Portuguese teenager midfielder Renato Sanches, who has overcome a cold, and winger Douglas Costa, who picked up a knock during Saturday’s 3-0 win at Cologne, were both on the flight to London.
- No club has progressed in a Champions League knockout tie after losing the first leg by four or more goals.
- Since the beginning of 2003-04, Arsenal have lost just 10 of their 62 home games in the Champions League, however, six of those defeats have come in the knockout stages.
- Four of Arsenal’s last six Champions League defeats at Emirates Stadium have come in the last 16, with two of those losses coming at the hands of Bayern Munich in 2013 and 2014.
- This is the 12th meeting between these sides in the Champions League, Bayern have won six of the previous 11 games with Arsenal winning three.
- The German side have won just one of their last six Champions League away games, losing three and drawing twice in that run; however, their three defeats all came by a single goal.
- Arsenal’s last 14 goals in the Champions League have all come from inside the box, including one penalty.
- Only Lionel Messi (10) and Edinson Cavani (seven) have scored more goals in the competition this season than Robert Lewandowski (six); the Polish striker has scored in just two of his last 12 away games in the Champions League however (four goals in total).