Limpopo police spokesman Lieutenant Mohale Ramatseba said the baby's mother was admitted to the local hospital when the child was raped by her father.
The incident was allegedly committed at Mamone village between last Tuesday and Saturday.
Ramatseba said the mother of the baby was later discharged from hospital and realised that her daughter was bleeding from her private parts when she was bathing her.
"The mother took the child to the doctors, who it confirmed that the child had been penetrated."
The suspect is expected to appear in the Nebo Magistrate's Court today and police investigations are continuing
The incident has angered the Commission for Gender Equality, which described the alleged incident as inhuman, merciless and brutal.
National gender spokesman Jabu Baloyi pleaded with the South African Police Service to hand over the investigation to police officers with a great track record in an effort to investigate the case with precision.
"It is quite unthinkable that we still have such people in our society," he said.
"If the allegations are found to be true the suspect must receive harsh punishment that will serve as a deterrent to others," he said.
The ANC Women's League in Limpopo was equally perturbed about the allegations.
"We have developed a keen interest in the matter and hope it gets the attention it deserves from the police, justice system, government, residents of Limpopo and all formations," ANC Women's League provincial chairwoman Maite Marutha said.
"We hope the man rots in hell if it is proved that he raped the baby," she added.