The case against Mlungisi Mtshali was postponed to November 22 for further investigation.
Mtshali appeared in the dock with a brown towel over his shoulders and his arms behind his back when the charges were read to him. His legs were in chains.
He told the court he did not intend to apply for bail and would apply for legal aid.
National Prosecuting Authority spokesperson Mthunzi Mhaga said that Mtshali would be kept at a high-security facility.
"If he was released on bail, he might interfere with the investigation."
Mhaga said Mtshali was facing several charges of kidnapping, rape and robbery and there was a possibility that more charges could be added.
"He is facing 21 counts of rape and more could be added as people come forward."
Targeted young black women
Mtshali was arrested on Friday, in KwaMashu outside Durban in the KwaZulu-Natal province.
The Durban central dog unit and the Durban organised crime unit assisted Gauteng police in following the man's trail since he fled his home in southern Johannesburg just before police raided it on Wednesday morning.
He was alleged to have targeted young black women aged between 19 and 21 in and around the Johannesburg and Pretoria areas.
He allegedly approached a group of women and invited them to celebrate his birthday with him at a nearby restaurant or bar.
He later asked one of them to accompany him to fetch his sister or a friend, taking a metered-taxi into Hillbrow or central Johannesburg.
He then lured his victim to a hotel room under the pretext of fetching his sister or the friend, or his luggage, and then raped her.