The imperial couple's car was part of a 400-meter long motorcade consisting of 46 vehicles, carrying a number of dignitaries including Crown Prince Akishino, Crown Princess Kiko and Japanese Prime Minister Shinzo Abe.
However, the event had to be postponed as Japan made contact after the Hurricane, leaving almost 90 people dead.
The Japanese government estimates that 119,000 people attended Sunday's parade of 2.6 miles, according to public broadcaster NHK. Spectators stood in rows deep and waved Japanese flags as they watched the parade unfold on the streets of the capital.
"To witness this historic moment in my own eyes and to see the smile of the emperor and empress. I want to be in the foreground," Hiyori Okazaki, a spectator, said on Reuters. "I can't wait so came last night."
Toshiko Ito, who was visiting the capital with his wife, added: "Emotions have evolved and I'm excited that I'm about to cry."
Emperor Naruhito wore a tailcoat at the parade, while Empress Masako donated a white dress and tiara, which shone in the sunshine.
The parade was one of the final official events marking the Emperor Naruhito's ascension to the throne, which took place in May after his father Emperor Akihito, abducted three decades later at the helm. He became the first Japanese monarch to abdicate in two centuries.
The official ceremony of the Emperor Naruhito was held in October, at the one-century ceremony at the Imperial Palace in Tokyo.
In an elaborate series of rituals known as "Sokui no Rei," purple curtains are pulled to reveal Naruhito and his wife sitting on two ornately decorated thrones.