Akihiko Kondo, 35, spent ¥2 million (£13645.50) on a formal ceremony at a Tokyo hall to Hatsune Miku, an animated 16-year-old hologram with saucer eyes and lengthy aquamarine pigtails.
Mr Kondo's mother, along with all of is relatives, refused an invitation to her only son's wedding.
The softly-spoken groom said: 'For Mother, it wasn't something to celebrate.'
Around 40 guests watched as he tied the knot with Miku, present in the form of a cat-sized stuffed doll.
'I never cheated on her, I've always been in love with Miku-san,' he said, using a honorific that is commonly employed in Japan, even by friends.
'I've been thinking about her every day,' he told AFP a week after the wedding.
Since March, Mr Kondo has been living with a moving, talking hologram of Miku that floats in a $2,800 desktop device.
'I'm in love with the whole concept of Hatsune Miku but I got married to the Miku of my house,' he said, looking at the blue image glowing in a capsule.
'Drop dead, creepy otaku!'
He considers himself an ordinary married man - his holographic wife wakes him up each morning and sends him off to his job as an administrator at a school.
In the evening, when he tells her by cellphone that he's coming home, she turns on the lights. Later, she tells him when it's time to go to bed.
He sleeps alongside the doll version of her that attended the wedding, complete with a wedding ring that fits around her left wrist.
Mr Kondo's marriage might not have any legal standing, but that doesn't bother him.
He even took his Miku doll to a jewellery shop to get the ring.
And Gatebox, the company that produces the hologram device featuring Miku, has issued a 'marriage certificate', which certifies that a human and a virtual character have wed 'beyond dimensions'.