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The 43-year-old man, who cannot be named to protect the identity of the girl, was found hanging from a tree at Mganduzeni, near Masoyi in Mpumalanga.
Masoyi police spokesperson Inspector Jiyela Sibiya said the man's body was found by his relatives, who then alerted the police.
"The man, who was staying in Marite village in Bushbuckridge, disappeared from his home after he discovered that his daughter had opened a rape case against him.
"He had been on the run since Thursday last week because he was aware that the police were searching for him. On Friday night he went to his grandmother's house to hide. On arrival he found the police talking to one of his relatives.
"When they tried to arrest him, he fled into the nearby bushes," said Sibiya.
It is alleged that he started raping her in 2005 when she was still 12. The man allegedly continued until last week.
She reportedly ran away from the RDP house where she was living with her father to alert her relatives about the alleged rape.
Her relatives accompanied her to the local police station to report the matter.
She told police investigators that her father was raping her all the time because he did not have a girlfriend.
Sibiya said the girl was taken to a place of safety at Thulamahashe near Bushbuckridge.
The girl had been staying with her father after he separated from her mother.