Wouter Basson was found guilty on Wednesday of unprofessional conduct for acting unethically as a medical doctor during his time as the leader of the apartheid-era chemical and biological programme Project Coast and later Delta G in the 1980s.
Basson was not present at the hearing as he had an emergency with one of his patients in Cape Town, said his legal team.
However, the family members of his victims attended the judgment hearing.
Lizzie Sofolo's husband was abducted, drugged, tortured and killed in the late 1980s – with the use of drugs made by Basson.
"Today the truth has prevailed, it is clear that he used his knowledge as a doctor to kill innocent people," she said.
Maria Ntuli's son, Jeremiah, was one of 10 Mamelodi youths who left home to join the ANC's armed wing, Umkhonto weSizwe, in 1987.
In 1996 the Truth and Reconciliation Commission heard that the group was drugged and put into a Kombi that was crashed into a tree and exploded.
"We just want this case to be over with now. It has been dragging on for years now, why doesn't it just end?" said Ntuli.
The Health Professions Council of South Africa's (HPCSA) inquiry into Basson's conduct during apartheid has been on-going for six years now.
The judgment was made by the HPCSA's professional conduct committee chairperson Jannie Hugo in Pretoria.
Basson, who is now a private cardiologist, was found guilty of coordinating the production of and stockpiling of mandrax, ecstasy and tear gas "on a major scale".
During this time, Basson provided "disorientating substances used for over border kidnapping" and supplied cyanide capsules to operational officers to use to commit suicide in case they were caught.
"The committee rejects that ethics have to be interpreted in the context of the time, medical ethics are the same during peace and war," said Hugo.
HPCSA registrar and chief executive Buyiswa Mjamba-Matshoba said she was unable to comment on what the appropriate sentence would be for Basson except that "the sentence will be in line with the charges".
Mjamba-Matshoba said that she was "very happy that justice has been done and that ethics have been upheld in this profession".
"Dr Basson kept on saying he acted as a soldier, but during this time he kept the registration of the HPCSA and that binds him to the council's values," she said.
His sentencing will take place in February 2014.