The 24-year-old, who cannot be named until he enters his plea, is accused of raping the teenager in the toilets of a bar in Johannesburg.
Earlier in the week, the family of the alleged victim said that Mr Mandela's ex-wife, Winnie Madikizela-Mandela, had sent her bodyguard to dissuade them from pressing charges.
The Mandela family has not commented.
Senior members of the Mandela family, including the former president's daughter Makaziwe Mandela, were in court during a brief hearing.
His bail application has been postponed until Tuesday, meaning he cannot legally be named until then.
He has been in custody since his arrest on Saturday.
The BBC understands that he will argue that it was consensual sex and he didn't know that his accuser was underage since the pub did not allow under-21s on its premises.
Under South African law, sex with someone under 16 is classed as rape whether consensual or not.
BBC Southern Africa correspondent Karen Allen says the family of South Africa's first black president have found themselves constantly in the public spotlight.
Just three months ago, another of his grandsons, Mandla Mandela, was given a suspended sentence after being convicted of assault, following an attack on a teacher after a road rage incident.