According to the Berliner Morgenpost newspaper, protesters marched with Palestinian, Syrian, Hezbollah and Iranian flags.
About 500 policemen were deployed to ensure security during the march, the newspaper said.
Counter-protesters also showed up to the rally to show their solidarity with the Israeli community. According to the newspaper, their rally gathered about 1,000 people.
READ MORE: Iranian President Attends Quds Day Protests Against Israel (PHOTOS, VIDEOS)
On Friday, prior to the rally, German President Frank-Walter Steinmeier urged Germans to oppose anti-Semitism.
Last week, Germany's anti-Semitism commissioner, Felix Klein, advised the country's Jewish community to avoid wearing yarmulkes, the traditional Jewish head covering for males, in public spaces due to the rise of anti-Semitic crimes.
The Quds Day (Jerusalem Day) rally, officially titled "For a Just Peace in Palestine," was started in Iran in 1979 and traditionally takes place on the last day of the Muslim holy month of Ramadan. On Friday, during the Quds Day rally in the capital of Iran, protesters burned the Israeli flag and effigies of Israeli Prime Minister Benjamin Netanyahu to express their discontent with Israel's claim to Jerusalem.