On Sunday, police in Taegu arrested the 22-year-old, identified only by his surname, Chung, after finding his child's body in a suitcase wrapped in a trash bag near his home. Chung had reported the boy missing.
Police initially believed the unemployed man had left his son to starve to death by abandoning him for 10 days while playing games.
Chung later confessed to "covering the child's nose and mouth with his hand," more than a month ago, killing him so that he could go to an Internet cafe, a police officer said.
The whereabouts of the child's mother was not clear, although news reports said she had been away for some time working in a factory.
South Korean television aired footage of Chung that showed him getting into a lift with a suitcase and checking his hair in the mirror, apparently on his way to dispose of his son's body.