A group of German Maccabi Haifa fans were subjected to anti-Semitic insults during the match at Berlin's Olympic Stadium, according to a statement from Union Berlin published Friday.
"This behaviour is shameful and we won't tolerate it. We apologise to those affected. Anti-Semitism is unfortunately still present in our society, which is why it also shows itself in the stadium," said club president Dirk Zingler in the statement.
"However, we will never tolerate discrimination in our ranks. It is important to remain vigilant and to work tirelessly against it."
Zingler said the club would support police investigations into the incident.
Beer was thrown at the group of Maccabi Haifa fans, who were also subjected to anti-Semitic insults and threats of violence, according to a press release from the German-Israeli Society Youth Forum.
One Union Berlin supporter allegedly tried to burn an Israeli flag, it continued.
Other Union Berlin supporters stepped in and swapped seats with the Maccabi Haifa fans.
The youth forum thanked those fans for their solidarity and said they were satisfied with the club's quick response.
Anti-discrimination network FARE also published a photo purporting to show a Union Berlin supporter making a Nazi salute at the game on its Twitter account.
"This man made nazi salutes towards the Maccabi fans and abused those who called him out," reads the tweet.
Maccabi Haifa did not comment on the incidents, instead thanking their opponents for their hospitality in a tweet.
CNN has contacted Maccabi Haifa, UEFA and Berlin Police for comment.
The match, which the German side won 3-0, was a symbolic affair, marking the first time that an Israeli team had competed in the Olympic stadium, which was built for the 1936 Olympic Games during the Nazi era.
Union Berlin normally play their home matches at the Stadion an der Alten Försterei.
However the ground doesn't meet the requirements for UEFA's European competition matches, so the game was played at the Olympic Stadium.
The number of anti-Semitic incidents in Germany has been growing steadily in recent years, Deutsche Welle reported in February.
There were at least 2,275 anti-Semitic crimes in the 12 months to the end of January 2021, some 55 of which were violent, it reported.