A march organised by the group United for Palestine drew around 3,500 people to the capital as it set off from a square between the chancellery and parliament, said police.
Many denounced Germany's arms exports to Israel, carrying banners and placards condemning Berlin's military support.
For decades, Germany has seen resolute support for Israel as a fundamental duty largely because of Nazi Germany's responsibility for the genocide of millions of European Jews during the Holocaust.
"I find it really terrible that Germany finds it so difficult to criticise Israel," a student told AFP, who asked not to be named.
Police deployed a large force of 1,400 officers to handle this and other rallies in the capital.
A ceasefire began a year ago and although Israel has reduced its level of attacks it has kept striking Gaza on a near-daily basis.
Strikes have killed some 1,450 Palestinians since the ceasefire, according to Gaza's health ministry.
Thousands more also marched in similar protests in London and Dublin.
Saturday's protests came three days after the third anniversary of the October 7, 2023 attack.
The attack was the deadliest in Israel's history, resulting in the deaths of 1,221 people, according to an AFP tally based on official Israeli figures.
Militants also dragged 251 hostages into Gaza, 44 of them already dead.
In response, Israel launched a military offensive that has left most of Gaza in ruins and killed more than 74,200 people, according to Gaza's health ministry.