Although politicians have largely taken a back seat in the anniversary, Mr Havel, incumbent Czech President Vaclav Klaus, Prime Minister Jan Fischer and a crowd of hundreds lit candles and laid flowers at the monument marking the site of the brutal clash.
"The march set history into motion," said Mr Havel to applause.
Marchers later saw a concert in the city centre featuring Mr Havel and US folk singer Joan Baez.
In a speech to the Czech senate earlier on Tuesday, Mr Havel paid tribute to the memory of those who had helped to bring down the Communist regime, including his late wife Olga.
"We often tend to forget our fellow colleagues, friends and the open-minded people in everyday life," he said, going on to name dozens who had died since the protests.
In a statement, US Secretary of State Hillary Rodham Clinton also joined in the praise, saying: "I congratulate the Czech Republic and Slovakia on 20 years of democracy and reaffirm the commitment of the United States to our strong alliance."
At a Prague concert organised by Mr Havel over the weekend, US President Barack Obama broadcast a video message saying: "Your spirit, your courage inspired the world."
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