The Duke of Cambridge spent about 40 minutes taking part in the ritual at Hama Rikyu Gardens.
He is on a week-long trip to China and Japan where he will undertake engagements to promote UK relations with both countries.
In his first visit to Japan, Prince William also took a speedboat ride to Tokyo Bay, which will host much of the 2020 Summer Olympics.
The last time a major member of British royal family visited Japan was in 2008, when Prince Charles came with his wife Camilla.
Hundreds of students and school children waving British and Japanese flags waited in the rain to greet him.
Kate Middleton is not with Prince William as she is due to give birth to their second child in April.
On the first day of his tour Prince William visited the Nakajima tea house, built 350 years ago in Japan’s Edo period, in the middle of a small lake within the Hama-Rikyu gardens.
As he entered the tea house, Prince William removed his shoes like the other guests, which included Tokyo governor Yoichi Masuzoe.
Dr. Genshitsu Sen, who is 92 and the 15th generation of his family to hold a senior role in the spiritual art of tea making, performed the traditional ceremony.
He also made tea for Prince William’s parents, Prince Charles and Princess Diana, when they visited Kyoto in 1986. Close to 100,000 people flocked to a parade in Tokyo at the time, as so-called “Diana Fever” swept the nation.
A number of gifts were given to Prince William, including a box of crackers, a book about the tea ceremony and a modern tea bowl decorated with a horse design in celebration of Prince George.
On February 27, Prince William is due to meet fellow royals Emperor Akihito and Empress Michiko at the Imperial Palace.
In this his first visit to Japan, Prince William will also be taken to the areas devastated by the 2011 tsunami and meet survivors.
In Shanghai, Prince William will launch the three-day Great Festival of Creativity at the city’s Long Museum on March 2.
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