Naruhito's father, Akihito, 85, abdicated on Tuesday in a simple ceremony, nearly three years after he first expressed fears that advancing age might make it difficult for him to perform his duties. It was the first abdication in 200 years.
Pledging to work as a symbol of the people, Naruhito, 59, was formally invested as emperor the day after.
People queued for hours to see the new emperor and his family stand on a palace balcony and wave to the gathered crowds. Normally such greetings take place during the New Year's holiday and on the emperor's birthday.
"I pray for your health and happiness," said the emperor, reading prepared remarks. "And I sincerely wish for further development of our nation by going hand in hand with other nations and seeking global peace."
Masako, wearing a yellow dress and hat, waved and smiled to the crowds along with other imperial family members.
They will greet the crowds six times on Saturday, according to public broadcaster NHK.