The man, who is her neighbor, told security officials he left with her on Tuesday after she complained that her family was verbally abusing her.
They were found at her extended family’s home just before midnight that same day.
Police spokeswoman Captain Nqobile Gwala said charges of kidnapping and rape had now been opened and under investigation.
She told The Times Live: “Charges of kidnapping and rape were opened for investigation Thursday at the Verulam SAPS (South African Police Service).
“The case has been transferred to the Phoenix Domestic Violence, Child Protection and Sexual Offenses Unit for further investigation.
Rusa’s manager Prem Balram had previously said he took the girl to ‘spoil’ her on her birthday.
Mr Balram added: “Reaction officers traveled 156 km from Rusa’s headquarters to Richards Bay after receiving several reports from area residents regarding the missing persons.
“Reaction officers located a house and found it with an extended family.
“According to the man, he left his home to spend the child’s birthday with his family.
“The child turned 13 on Tuesday and said he intended to spoil her on her birthday and wanted to look for a job in the area during the week. ”
A family member claimed to have seen the teenager get into her neighbor’s car just before she disappeared.
Her family went to the home of the father of four while looking for their daughter, only to find that he was missing.
The girl’s parents have previously said they are friends with the neighbor, Times Live reported.