Such values "must always be lived out and defended anew," Merkel told political leaders and European guests at a ceremony, warning that these freedoms cannot be taken for granted.
Speaking in the Reconciliation Chapel on the former "death strip" that ran alongside the wall, the chancellor said that the barrier that divided communist East from democratic West was "history".
Merkel herself grew up in East Germany and was a scientist working in Berlin on November 9, 1989.
That the communist authorities finally opened border crossings that day "teaches us that no wall that shuts people out and limits freedom is so tall or broad that it cannot be broken through," Merkel said, AFP reported.
The chancellor and guests including the presidents of Poland, Hungary, the Czech Republic and Slovakia had earlier been invited to stick roses through holes in a section of wall still standing at the Bernauer Strasse memorial, just north of central Berlin.
Groups of schoolchildren from around Europe, including war-torn Ukraine, also spoke in their native languages to the leaders about the emotions the anniversary wakens for them.