Tsafendas was born in Lourenço Marques (today's Maputo) to Michaelis Tsafendas, a Greek seaman, and Amelia Williams, a Mozambican of mixed race. He was raised by his grandmother. At the age of ten, he moved toTransvaal, returning to Mozambique four years later. Tsafendas was shunned in white circles in Southern Africa because of his dark skin, though under the Apartheid system's racial laws he was classified as white.
During the 1930s, Tsafendas joined the Communist Party. He became a seaman in the merchant marine in 1941. By this time, symptoms of schizophrenia had already begun to manifest. He was hospitalized several times in various countries due to outbreaks of irrational behavior.
He had become a baptised member of the Twos by Twos sect while visiting Greece, and associated with its members after returning to South Africa on a temporary visa.
In 1966, Tsafendas obtained a temporary position as a parliamentary messenger. A month later on 6 September, Prime Minister Verwoerd entered the House of assembly and made his way to his seat. Tsafendas approached him, drew a concealed knife, and stabbed Dr. Verwoerd multiple times in the chest before he could be pulled away by other members of parliament.
Following the assassination, he was disowned by the Two by Twos church.
At the trial, Judge Andries Beyers declared Tsafendas not guilty of murder by reason of insanity. He had been diagnosed as being schizophrenic and it was claimed by police that he had said that he had a giant tapeworm inside him, which spoke to him. The court ordered that he be detained "at the pleasure of the State President", which meant that only the State President (later President) had the authority to release him. He was never released.
Tsafendas was at first given a cell on death row in Pretoria Central Prison, next to the room in which men were hanged, sometimes seven at a time. In 1986, he was transferred to Zonderwater Prison near Cullinan. In 1994, he was transferred again, this time to Sterkfontein psychiatric hospital outside Krugersdorp, where he died at the age of 81.
Tsafendas died in October 1999 of pneumonia aggravated by chronic heart failure. His funeral was held according to Greek Orthodox rites, and he was buried in an unmarked grave outside Sterkfontein Hospital.
An award-winning play entitled Tsafendas by Anton Krueger was presented to South African audiences in 2002. A London production entitled . was written by the noted Shakespearean actor Anthony Sher, who had lived in Cape Town at the time of the incident. I.D. premiered at the Almeida Theater in London in 2003, followed by an American debut in 2005.