The Seoul Western District Court ordered feeding and ventilator tubes to be removed from the 75-year-old woman identified only as Kim, saying she has no chance of recovery.
The landmark ruling acknowledged an individual's right to die for the first time here, but rekindled debate on euthanasia.
The current law bans any form of assisted suicide and sees the removal of a respirator from brain-dead patients as murder.
Kim was declared brain-dead at Seoul's Severance Hospital in February after she sustained brain damage and fell into a coma while undergoing a lung examination.
Three months later her children filed a court petition after the hospital rejected their request that she be allowed to die in peace and with dignity.
The family claimed that extending Kim's life using medical devices would prolong her "painful and meaningless" existence.
"The patient can ask doctors to remove life support if it causes physical and mental pain and hurts human dignity and personality," Judge Kim Chon-Soo said in his ruling.
He said the family's request should be accepted in consideration of Kim's "hopeless state with no chance of recovery" even if she could not herself express her desire.
"Considering her hopeless state, the expected years left in her life and her age, the patient is assumed to have expressed her wish to die a natural death with the respirator removed," the judge said.
However, he stressed that his ruling is limited to those for whom medical treatment has no impact and who are presumed to want to stop treatment.
Local religious communities have been split on the subject of euthanasia.
In 2004 a family was convicted of murder for removing life support systems from a brain-dead relative. A doctor was charged with aiding murder.
Last year a father was given a four-year suspended jail term for the removal of a respirator from his brain-dead son.