The Imperial couple's car was part of a 400-meter motorcade consisting of 46 vehicles carrying a number of dignitaries, including Crown Prince Akishino, Princess Kiko, and Japanese Prime Minister Shinzo Abe.
However, the event had to be postponed as Japan dealt with the aftermath of typhoon Hagibis, who left nearly 90 people dead.
The Japanese government estimates that 119,000 people attend Sunday's parade, which stretches for 2.6 miles, according to public broadcaster NHK. Spectators stood in rows deep, waving Japanese flags as they watched the parade progress along the streets of the capital.
"To witness this historic moment with our own eyes and see the smile of the Emperor and the Empress. I wanted to be in front," viewer Hiyori Okazaki told Reuters. "I couldn't wait, so it came last night."
Toshiko Ito, who visited the capital with her husband, added: "The emotion is welcoming and I was so happy I would cry."
Emperor Naruhito wore fur during the parade, while Empress Masako donned a white dress and tiaras that shone in the sunlight.
The parade is one of the final official events marking the Emperor Narukhito's accession to the throne, which officially took place in May after his father, Emperor Akihito, abdicated after three at the head. He became the first Japanese monarch to abdicate in two centuries.
The official ceremony of the enthronement of Emperor Naruhito took place in October, a century-long ceremony at the Imperial Palace in Tokyo.
In a complex series of rituals known as "Sokui no Rei", purple curtains were pulled back to reveal Naruhito and his wife sitting on two ornate thrones.
] Emperor Naruhito wore a rust-colored gown for the ceremony, and Empress Masako wore a colorful white robe and traditional hair with a gold head.
At the ceremony, Emperor Naruhito proclaimed his introduction to the public by the imperial family and international dignitaries.
"I hereby promise to act in accordance with the Constitution and to fulfill my responsibility as a symbol of the state and unity of the people of Japan, always wishing the happiness of the people and the peace of the world, turning their thoughts to the people and standing up