Court papers reveal police found both bloody weapons in the larney house at the De Zalze Golf Estate on the morning of January 27, 2015.
The 21-year-old is accused of slaughtering his father Martin van Breda, 54, his mother Teresa, 56, and brother Rudi, 22, with an axe, and attempting to murder his little sister Marli, now 18.
He was also charged with obstructing the ends of justice for lying to police and tampering with evidence.
Van Breda handed himself over to police on the instruction of his defence attorney, Piet Botha, before police could arrest him on Monday.
He was released on R100 000 bail at the Stellenbosch Magistrates Court on Tuesday.
Medical experts indicate that he exhibited “self-inflicted” wounds made by a knife.
It is believed that Marli, who sufferes from retrograde amnesia, holds the key to what really happened on the fateful night.
National Prosecuting Authority spokesman Eric Ntabazalila says DNA evidence will prove that Henri was the killer.
“We are aware of the fact that some people think that we might have taken too long, we made sure we had enough evidence to take the case to court,” he said.
According to the charge sheet, witnesses heard raised voices coming from the Van Breda home that evening.
At approximately 4:24am, the accused called his girlfriend from his cellphone, the call went unanswered.
Three minutes later he Googled emergency numbers.
However, he made the call only two and a half hours later.
Police found his parents and brother dead at the scene, while Marli was rushed to hospital with life-threatening injuries.
Post-mortem examinations found the three died of severe head injuries.
Court papers state: “The accused was found at the scene, he was dressed in a pair of sleep shorts and white socks. DNA analysis of blood found on the accused and on his clothing matches the DNA of the three deceased.”
Henri is to appear in court on September 9.
Meanwhile, Henri's best friend claims he is a "genius" with an IQ "way above 145".
Alexander Boschoff, 20, says he has known the triple murder accused for years and even spent a holiday with the Van Breda family two weeks before the gruesome murders at their Stellenbosch home last year.
Boschoff described Henri van Breda as “very clever”.
“In fact, he is a genius. His IQ is way above 145. While we were on holiday, we spoke about higher grade mathematics because it was a subject we both found very interesting,” he said in an interview with the Cape Times.
By comparison, math geniuses Albert Einstein and Stephen Hawking both have IQs of 160.
Boschoff adds: “Henri’s manner of thinking is way above that of a normal person. Our families often spent holidays together. We have known each other for years.”
Boschoff, who is currently studying law and accounting at Stellenbosch University, said the Van Bredas were a “typical happy family”.
“When the attack happened, I just couldn’t make sense of it because, on the surface, nothing was wrong. They seemed like the perfect family,” he said.