A video taken on Christmas Day showed three middle-aged white men struggling with two boys in a swimming pool at a holiday resort in the central city of Bloemfontein and trying to strangle, slap them or dunk their heads underwater.
The violence allegedly broke out after the men stopped the cousins from using the pool, saying it was reserved for resort clients.
Jacobus Johannes Classen appeared at a Bloemfontein court and was released on bail, the National Prosecuting Authority (NPA) said in a statement on Thursday.
He was charged with attempted murder, assault and crimen injuria, an offence that means inflicting humiliation through obscene or racially-offensive language.
The two other suspects appeared in court on Wednesday on assault charges and were released on warning, the NPA added. The case has been postponed to January 25.
Brian Nakedi, the father of one of the boys, told national broadcaster SABC the teenagers asked him for help because they were "being prevented from swimming by old adult males, who happen to be white."
The men "said there was a miscommunication" as they did not know the boys were also booked in at the resort, and the matter appeared to be settled, he added.
"But as we were leaving, the boys arrived and tried to swim, that's when the scuffle erupted."
Some there said the men inferred the facility was for white people only, as in the apartheid era.
Bloemfontein is located in Free State, a region known for persistent racial tensions.
South Africa remains deeply divided along racial lines almost three decades after Nelson Mandela came to power vowing national reconciliation following the end of white-minority apartheid rule.
South African President Cyril Ramaphosa on Tuesday said it was "deplorable that adults dealing with teenagers resort to violence with such disturbing ease."
"We must be united in ridding our society of the violence we see in the videos of the incident at the Free State resort, whether such violence comes with racism or not," he added.