The 23-year-old wore the same black and grey striped T-shirt he wore to court last week.
He avoided making eye-contact with people in the public gallery, and looked down at his hands and fiddled with them during the proceedings.
He has now been provided with a legal aid lawyer, Pieter van Niekerk.
Van Niekerk indicated that his client had chosen to remain silent and would not apply for bail.
He has due to undergo DNA testing and to plead.
The case was postponed to March 13 for further investigation.
Among those attending the hearing on Monday was Women, Children and People with Disabilities Minister Lulu Xingwana.
Like many of the protesters at the court, she wore a pink blouse over a pink skirt. The girl was wearing a pink top the day she was murdered.
She was reported missing on Saturday, December 28 and, after questioning by the police, her uncle apparently confessed to the crime.
He showed the police the girl’s body underneath a bed in her father’s flat.
Her parents are divorced and the father reportedly left her in the man’s care while he spent time with his girlfriend.
Last Monday, National Prosecuting Authority spokesman Mxolisi Nxasana expressed confidence in the case against the man.
“It’s a watertight case and we are certain that we will make a conviction,” he said.
Hundreds of people attended the girl’s memorial service held in the city last week. Many called for justice.
The girl was cremated last week and her mother had said she intended to scatter her daughter’s ashes in the ocean.