The 10-year-old Verulam girl, who was allegedly raped by her stepfather for the past five years, has been taken to a place of safety, the KwaZulu-Natal Department of Social Development said on Wednesday.
Spokesperson Vukani Mbhele told News24 that the girl would receive "psychosocial support".
Ngidi said this meant she would be given mental, emotional, social and spiritual support to help her reintegrate into society.
KwaZulu-Natal police told News24 via email that the man was set to appear in the Verulam Magistrate's Court on Thursday after he was arrested on Tuesday.
He is being detained at the Verulam police station and is facing a rape charge.
Ngidi said the department was also planning to take the girl back to school once she was "rehabilitated".
"Obviously once we have established that she is responding positively to her therapy, and that she has been fully rehabilitated, we will make sure that she is enrolled at school. According to the South African Constitution, every child has a right to go to school," he said.
The girl had allegedly been raped by her stepfather since her mother's death five years ago.
According to private security company Reaction Unit South Africa, the stepdad had allegedly sealed all the windows in their home and held her captive in the house while he was at work.
He also allegedly did not enrol her in school, so that she would not tell anyone about the rapes and abuse, RUSA's Vinod Singh said.
News24 reported on Tuesday that sex toys, lingerie and pornographic material were strewn around the stepfather, who had been severely assaulted by the Verulam community on Monday as a result of the allegations.
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