Surrounded by an escort team riding 16 motorcycles, the royal couple set out in a convertible Toyota Century sedan, especially remodeled for the occasion which was fitted with white tapestries and its height and angles designed to help spectators get a better view of the royals over the 4.6-km long route, Efe news reported.
According to estimates, more than 100,000 people gathered along the route, waving the national flag and taking photos of the parade, which lasted half an hour. Many had travelled from across the country to witness the occasion.
This was the first parade held by the couple since their 1993 wedding and following the official enthronement ceremony on October 22.
The ceremony had been postponed due to the damage caused by powerful Typhoon Hagibis, which killed dozens of people and caused significant damage in eastern and central Japan, and in consideration for the victims' families.
Many people had been unable to watch the enthronement ceremonies because of power outages due to the typhoon damage.
The convertible used by the royal couple was followed by cars carrying the Emperor's brother, Crown Prince Fumihito, and his wife Crown Princess Kiko, as well as Prime Minister Shinzo Abe.
In total, 46 vehicles, including official cars and escort motorcycles, were part of the 400-meter long motorcade, which started from the Imperial Palace and passed by iconic locations such as parliament before ending at the official residence in Akasaka.
Authorities deployed around 26,000 officers and established extensive security measures, including around 40 checkpoints along the route, blockades on nearby roads and restrictions on using metro stations in the area.
Naruhito ascended the Chrysanthemum throne on May 1, a day after the first abdication in the country in more than 200 years by his father Akihito.
However, the official proclamation of his enthronement was carried out in October, in a ceremony equivalent to a coronation.
The enthronement was attended by around 2,000 guests, including Japanese dignitaries, heads of states from across the world and other international representatives.