The ribbon-cutting ceremony attended by dignitaries and family took place on what would have been his 76th birthday.
More than 80,000 people signed a petition calling for the name change to honor the dissident playwright.
Foreign Minister Karel Schwarzenberg said he hoped every Czech air passenger leaving Prague would think of the man to whom they owed their freedom.
“This is the right place [to bear Vaclav Havel’s name] – it was he who enabled the Czech nation to travel out of this country,” he added.
Vaclav Havel led the peaceful 1989 overthrow of communism in then Soviet-backed Czechoslovakia.
“November 1989 was possible only because of Vaclav Havel,” said Karel Schwarzenberg.
A line of dignitaries including the former president’s widow Dagmar Havlova cut the small strip of airport tape to mark the renaming.
Dagmar Havlova said: “To me, today’s ceremony is proof of recognition of President Vaclav Havel, a recognition of freedom and democracy in our country, a recognition of his acts for this country. Ladies and gentlemen, welcome to the Vaclav Havel Airport Prague.”
The airport – one of the busiest transport hubs in central Europe – was formerly known as Ruzyne airport.
Vaclav Havel became president of Czechoslovakia in 1989 after the fall of communism. When Slovakia split in 1993, he remained Czech leader until 2003.
Vaclav Havel died last December after having suffered from respiratory problems for many years.
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