Born into a diplomatic family and educated at Harvard, Empress Masako left behind a promising diplomatic career to marry into the royal family.
Naruhito, 59, officially succeeded his father in May, but a series of ceremonies and rites celebrating his enthronement are being held last month, this month and later this year.
Japanese Emperor Naruhito and Empress Masako rode through central Tokyo on Sunday in a motorcade to mark this year's imperial succession as well-wishers waved national flags and held up mobile phones for snapshots of the smiling royal couple.
Security was high for the event, with long lines forming hours ahead of the parade and thousands of police deployed to search bags and move spectators through metal detectors.
The royal couple emerged from the palace moments before 3: 00 pm (0600 GMT), with the Emperor wearing formal Western clothing and the Empress dressed in a long cream gown and jacket, wearing a tiara passed down by her predecessor.
On Sunday, the royal couple will parade in a convertible auto along a 4.6-km route from the palace to their residence in central Tokyo to mark the enthronement.
The motorcadewas led by a black Century limousine from Toyota Motor.
The parade of almost 5km through central Tokyo was originally scheduled for Oct 22 as part of a series of events marking the official proclamation of Emperor Naruhito's enthronement.
An estimated 119,000 people came to watch the parade Sunday, local media reported. Some experts say the government's funding of the Shinto harvest ritual could violate constitutional separation of state and religion.
Emperor Naruhito expressed gratitude to about 30,000 well-wishers who gathered at the entrance of Imperial Palace in Tokyo on November 9 in a festive event celebrating his accession to the throne. After the parade, it will be put on display in Tokyo and Kyoto.
"The sky is so blue and this is a great day for taking photos, as if it's the heaven's blessing for (the emperor)", said Suzuki, an amateur photographer.
"Emotion welled up and I was so happy that I was about to cry", she said. In the previous such ceremony, Rolls-Royce Corniche III was used.
Naruhito, who studied at Oxford, is a historian, a viola player and an expert on water transport. She developed "adjustment disorder" after giving birth to the couple's only child, Princess Aiko, and facing pressure to produce a boy in Japan's monarchy.
"I am grateful to you gathering here today for your congratulations", Naruhito told a flag-waving crowd, standing on a stone bridge at the palace with Empress Masako following congratulatory speeches by Prime Minister Shinzo Abe and other notable figures.