Police said that around 800 protesters, largely young Palestinian men, gathered at Potsdamer Platz in central Berlin shortly before 6pm to demonstrate against Israeli military action in the Gaza Strip.
They then tried to reach the Fan Mile, the street running west from the Brandenburg Gate which is sealed off for World Cup games.
The protesters broke through the first police cordon, Tagesspiegel newspaper reported, and were stopped by a second police line.
Police said the protest then turned towards Wittenbergplatz.
Police reinforcements were rushed in to contain the demonstration and stones were thrown at officers, Tagesspiegel reported.
There was also trouble in Frankfurt am Main where 2,500 pro-Palestine demonstrators gathered on Saturday.
The Frankfurter Allgemeine Zeitung reported that 50 police officers struggled to keep the protest under control and had to use pepper spray against demonstrators. Several arrests were made.