Proceedings were being held in camera as the boys, both 16, are minors.
The teenagers arrived in court with their feet chained together.
They wore jeans and sweaters, and bowed their heads as a police officer led them into the children's court.
Their faces were exposed, unlike their first appearance last week when they had their faces covered with a blanket.
They face murder charges after Thandeka Moganetsi, 15, and Chwayita Rathazayo, 16, were found dead in a field in Dobsonville last week.
The girls were dressed in George Khosa Secondary School uniforms and had cuts on their hands and necks.
Three black candles and two new razor blades were found at the scene.
Rathazayo's uncle, Phumzile Booi, said she had marks on her hands and would hide them from the family.
"She had marks, as if a sharp object was used on her arms... but she would not show them to anyone," he said outside the court.
Rathazayo was a good child, loved sport and competed in swimming at provincial level, he said.
"She was obedient. She and Thandeka were very close. She actually wanted us to adopt her friend so that they could stay together."
Relatives of the boys sat quietly outside the courtroom and refused to speak to journalists. The girls would be buried in Dobsonville on Tuesday.