The 43-year-old piano teacher became so angry about a divorce from her online husband that she logged on to the MapleStory computer game with his password and deleted his digital persona.
It has prompted a debate among online gamers and bloggers about whether virtual offences should be punished in the real world.
The woman was arrested on Wednesday and taken 620 miles from her home in southern Miyazaki to be detained in Sapporo, where the man lives, police said.
The two are believed never to have met in the real world and the woman had not plotted any revenge outside cyberspace.
Police quoted her as saying: "I was suddenly divorced - without a word of warning. That made me so angry."
She was arrested on suspicion of illegally accessing a computer and manipulating electronic data.
The woman used login information she got from the 33-year-old office worker when their characters were happily married, and killed the character.
The man complained to police when he discovered that his beloved online avatar, the name for the characters used by gamers to respresent themselves in virtual worlds, was dead.
She has not yet been formally charged, but could face up to five years in prison or a fine of more than £3,000 if eventually convicted.
MapleStory players create and manipulate digital images called avatars - which represent themselves - while engaging in relationships and social activities and fighting monsters.
Bad online behaviour is usually dealt with within the rules set up by the developers of online worlds, which can ban miscreants or confiscate their virtual possessions. Virtual crimes, however, can also have real life consequences.
In August, a woman in Delaware was charged with plotting the real-life abduction of a boyfriend she met through the virtual reality website Second Life.
A 16-year-old boy in Tokyo was also charged with stealing the ID and password of a fellow player in order to swindle virtual currency in an online game. ~Telegraph.Co.UK
