The newlyweds are said to have expressed gratitude to the imperial family and people who supported them before leaving.
Mako, who turned 30 in October, announced her engagement with Komuro four years ago. But their union has been plagued by years of controversy, public disapproval and tabloid frenzy over a money scandal involving Komuro's mother.
At a press event after their marriage ceremony last month, the newlyweds apologized for any trouble caused by their marriage and expressed gratitude to those who supported them.
"To me, Kei is a very important, indispensable existence," Mako said.
"Mako and I would like to build a warm, nice family," Komuro said. "Happy times, unhappy times, we would like to be together, and we will be indispensable to each other."
In October, Komuro failed the New York state bar exam, but he said he will continue to study and retake the test in February.