Residents of Coligny took to the streets after the court decision, burning down a white family's home and heightening racial tensions that erupted after the teen's death.
Pieter Doorewaard, 26, and Philip Schutte, 34, are accused of killing Matlhomola Mosweu on April 20, after they reportedly caught him stealing sunflowers from a farm in the area.
The boy is alleged to have died after being thrown out of a moving vehicle driven by the pair and suffering a broken neck. A witness has claimed he was deliberately jettisoned.
The men claim he jumped off the truck as they were taking him to the police.
The death sparked rioting in the town, with black residents torching and looting white-owned shops. The accused later handed themselves over to the police.
Following Monday's arson attack on the white-owned property, a farmer pulled a gun on an AFP photographer at the scene and attacked him as he took pictures of the inferno. Another photojournalist, from a local newspaper, was also attacked and injured in the scuffle.
Magistrate Magaola Foso told a packed court room that he was aware of the tensions around the case but said he would not respond emotionally.
"There is no link between the said witness evidence and the two persons at this stage," he said.
The two accused were released on 5,000 rand bail ($369, 337 euros) and their case will resume on June 26.
Racially charged incidents between white farm owners and poor black farmhands and residents are common in South Africa.
Last year two white farmers in eastern Mpumalanga province allegedly forced a black man they accused of trespassing into a coffin. The case sparked outrage after a video of the alleged incident emerged on social media.
