The Bornholmer Strasse bridge was the first crossing to open on November 9 1989 after the announcement that East Germany was lifting travel restrictions on its citizens.
It was a pivotal moment in the collapse of communism in Europe.
Merkel, who grew up in East Germany and was one of thousands to cross to the West that night, recalled that "before the joy of freedom came, many suffered".
She lauded Gorbachev for his role in pushing for reform in the Soviet Union.
"You made [change] possible - you courageously let things happen, and that was much more than we could expect," Merkel told Gorbachev, winning applause and cheers from the crowd of several hundred on the bridge over railway lines.
She also welcomed to the former crossing Poland's 1980s pro-democracy leader, Lech Walesa, saying his Solidarity movement provided "encouragement" to East Germans.
Yesterday was the 20th anniversary of the border's opening. The wall kept East Germans penned in their "workers' paradise" for 28 years.
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