The usual rites of a royal wedding, including a lavish banquet, were almost entirely absent as a marriage that has divided opinion in Japan was sealed by a palace official submitting paperwork to a local office.
Mako, 30, later told a televised press conference their marriage, delayed three years and called unfit by some, “was a necessary choice to live while cherishing our hearts”.
“For me, Kei-san is a priceless person,” she said.
Mr Komuro responded: “I love Mako. I live only once and I want to spend it with someone I love.”
“I hope to have a warm family with Mako-san, and I will continue to do everything to support her,” he said.
Mako was earlier photographed leaving the palace for the ceremony wearing a pale blue dress and holding a bouquet.
The niece of Emperor Naruhito bowed outside the residence to her parents Crown Prince Akishino and Crown Princess Kiko, and her sister Kako, then the sisters hugged each other.
Mako and Mr Komuro were classmates at Tokyo’s International Christian University when they announced in September 2017 they intended to marry the following year.
However a financial scandal involving her new mother-in-law surfaced two months later and the wedding was suspended.
They are expected to move to the US where Mr Komuro, 30, works as a lawyer.
The move has drawn comparisons with Meghan Markle and Prince Harry - who stepped down royal duties and moved to California last year - earning the couple the nickname “Japan’s Harry and Meghan”.
Under Japanese law, female imperial family members forfeit their status upon marriage to a “commoner” although male members do not.
The couple made statements at a press conference in the afternoon but were not taking questions because Mako showed fear and unease at the questions that would be posed, the Imperial Household Agency said.
Mako is recovering from what palace doctors described earlier this month as a form of traumatic stress disorder that she developed after seeing negative media coverage about their marriage, especially attacks on her now-husband.
The financial dispute that hit the couple’s wedding plans involved whether money Mr Komuro’s mother received from her former fiance was a loan or a gift.
Mako’s father asked Mr Komuro to clarify, and he wrote a statement defending himself but it is still unclear if the dispute has been fully resolved.
Controversy in Japan over the wedding was only heightened last month when pictures emerged of Mr Komuro’s hair tied in a ponytail, which critics thought was unbecoming of someone set to marry a princess.
No longer a royal, Mako has now taken the surname of her husband.
Mako has also declined the 140 million yen (£893,000) dowry to which she was entitled for leaving the imperial family, palace officials said.
She is the first imperial family member since the Second World War to not receive the payment while marrying a “commoner” and chose to do so because of the criticism over her marrying a man some consider unfit for the princess.