0702 GMT November 19, 2019
The rituals cemented a transition that began with his father's abdication earlier this year, and drew royalty and political leaders from around the world, AFP reported.
A public parade for the event was postponed after a deadly typhoon, but the government went ahead with the granting of pardons for more than half a million people convicted of minor offences including traffic violations.
The main event took place in the Imperial Palace's Pine Room, where royal attendants drew back purple curtains hanging from two heavily adorned structures housing the imperial thrones, revealing the emperor and empress standing inside.
"I hereby declare my enthronement at home and abroad," Naruhito said, dressed in a voluminous draped robe topped with a copper overcoat.
Empress Masako, a Harvard-educated former diplomat, stood silently before her throne in a similar, smaller structure, wearing a multi-layered kimono and a highly stylized hairpiece.
Naruhito pledged to "pray for the happiness of Japanese people and world peace" and "fulfil my duty as the symbol of Japan and of the unity of the people of Japan."
He was later to host around 400 of the assembled royalty and dignitaries to a sumptuous banquet at the palace, before which the guests will be allowed to catch a glimpse of the throne and be treated to traditional Japanese court music.
Standing before him, flanked by royal family members also wearing heavily decorated traditional robes, Prime Minister Shinzo Abe promised the people of Japan would "respect your highness the emperor as the symbol of the state and of the unity of the Japanese people."
The Japanese royal family commands relatively broad support, although polls suggest the younger generation is less interested in the monarchy.
A poll released by national broadcaster NHK on the eve of the ceremony found 70 percent of voters in the country hold "friendly or favorable" views towards the imperial family.
But despite the support, the monarchy that is sometimes described as the world's oldest faces other concerns, particularly succession.
Emperor Naruhito and Empress Masako have one child, a 17-year-old daughter named Aiko. But imperial rules allow only a man to ascend the throne, and royal women lose their titles if they marry a commoner.