Around 3,500 people had gathered in the German capital's Neukölln district on Saturday afternoon in one of several rallies over the escalating conflict in the Middle East, according to police.
Protesters threw stones, bottles and fireworks as police tried to break up the demonstration, injuring 93 officers and prompting them to use pepper spray.
Several people were being investigated for shouting "anti-Israel slogans", the police said.
Around 900 officers were deployed to several demonstrations during the day, with the others passing mainly peacefully.
Palestinian militants have launched more than 3,000 rockets into Israel over the past week, according to Israel's army, which has launched hundreds of air strikes on Hamas and other Islamist groups in the crowded coastal enclave of Gaza.
The most intense hostilities in seven years were triggered by weekend unrest at Jerusalem's Al-Aqsa mosque compound, which is sacred to both Muslims and Jews.
Germany has seen several scattered demonstrations over the escalating conflict, with protesters shouting anti-Semitic slogans, burning Israeli flags and damaging the entrance to a synagogue with stones.
The Central Council of Jews in Germany on Sunday said it had received "a torrent of the most vile anti-Semitic insults" on social media.
READ ALSO: Germany's Jews call for protection amid Israel-Palestinian clashes
Council president Josef Schuster urged the police to take a hard line against anti-Semitism and said recent events had been "reminiscent of the darkest times in German history".
Interior Minister Horst Seehofer on Sunday said Germany would crack down hard on anyone found to be spreading "anti-Semitic hatred".
"We will not tolerate Israeli flags burning on German soil and Jewish institutions being attacked," he told the Bild am Sonntag newspaper.
READ ALSO: Germany slams 'anti-Semitic' demos and Hamas 'terrorist attacks'
Speaking at an ecumenical church congress, President Frank-Walter Steinmeier also said "nothing can justify" threats to Jews in Germany or attacks on synagogues.
Some six million Jews were murdered during the Holocaust under Adolf Hitler's Nazi regime.
The Jewish community in Germany has been growing since reunification in 1990, notably with the arrival of many thousands of Jews from the former Soviet Union.
The arrival of refugees from Arab nations hostile to Israel, in 2015 and 2016, added to the prevailing anti-Semitism in some Muslim circles in Germany.
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