The man whose name is being withheld for security reasons said through his lawyers that he did not want to be tried as a "Mandela" but as a "normal person". He cannot be named until he formally pleads to the charge.
The 24-year old is accused of raping the teenager in the toilets of a bar in Johannesburg. His bail was set at $535 (£340).
The BBC understands that he will argue that it was consensual sex and he didn't know that his accuser was underage since the bar 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.
The family of South Africa’s first black president has 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.
