Under Japanese law, female imperial family members forfeit their status upon marriage to a "commoner" although male members do not.
She also skipped the usual rites of a royal wedding and turned down a payment offered to royal females upon their departure from the family.
She is the first female member of the royal family to decline both.
The couple are expected to move to the US - where Mr Komuro works as a lawyer - after marriage. The move has drawn inevitable comparisons with British royals Meghan Markle and Prince Harry, earning the newlyweds the nickname "Japan's Harry and Meghan".
Like Ms Markle, Mr Komuro has come under intense scrutiny since his relationship with Ms Mako was announced. He was most recently criticised for sporting a ponytail when he returned to Japan.
Some tabloid newspapers and social media users felt his hairstyle - seen as unconventional in Japan - was unbecoming of someone set to marry a princess.
There was also a protest on Tuesday against the couple's marriage.