The New York edifice, whose official name is One World Trade Centre, takes the title as tallest after including the spire installed this year, which raises it from 417 meters to 542 metres, leaving the 442 metres of the Chicago skyscraper behind.
Once complete, the Freedom Tower will be the third tallest building in the world, trailing only the Burj Khalifa in Dubai and the Makkah Royal Clock Tower in Mecca, Saudi Arabia, the CTBUH said.
"The design of One World Trade Centre, as explained to us, reinforces its role as a symbol of resurgence on this important site," CTBUH executive director Antony Wood said.
The building stands on the site of the original Twin Towers of the World Trade Centre, destroyed in the terrorist attack of Sep 11, 2001.
Chicago's Willis Tower, formerly the Sears Tower, stands 130 stories high and is topped by an observation deck with a very popular bar and restaurant.
For many years New York retained the title for the tallest skyscraper in the world, thanks to the Empire State Building, but in 1974 the Sears Tower went up in Chicago and snatched that honour away.