A banner with the phrase "Gay Gunners" and a crude cartoon image of Arsenal player Mesut Ozil, who is German, was shown at the match against Arsenal in Munich. The English club's nickname is the Gunners.
The closure of one sector will come during the return leg of the Champions League quarterfinals against Manchester United on April 9.
A second banner with the slogans "Say No To Racism. Say Yes To Kosovo" was also displayed. Kosovo if a former province of Serbia whose proclamation of independence is disputed by Serbia.
UEFA fined Bayern 10,000 euros ($13,700) for displaying the "illicit banner."