The cardiologist, 63, now risks being barred from practising medicine after the council ruled that he had flouted ethical rules after a six-year inquiry.
Basson faced charges over supplying suicide cyanide capsules to operational officers, tranquilising substances for kidnappings, and for producing sedatives, ecstasy and tear gas.
"The breaches of medical ethics amount to unprofessional conduct," said Jannie Hugo, chair of a Health Professions Council of South Africa (HPCSA) investigative committee on the matter.
The charges stem from Basson's time working for the white minority state's chemical and biological warfare programme in the 1980s and early 1990s.
Basson, who had pleaded not guilty to all charges, was not present when the verdict was announced.
The committee rubbished his argument that he had acted during a war, had been under military orders, and had operated as a soldier and not a doctor.
He was held accountable to charges of producing "drugs and teargases on a major scale" and supplying mortars weaponised with teargas to Angola's civil war guerilla leader Jonas Savimbi.
Basson also was found guilty of providing "disorientation substances for over the border kidnapping" used to tranquilise abductees, and for making cyanide suicide capsules available to specialised units.
"He is evil. I agree with the committee when they say as a doctor Basson was there to serve people, not kill them," Lizzy Sefulo, 72, the widow of an apartheid-era victim, told the Sapa news agency.
Sefulo said her husband and three other anti-apartheid activists were drugged and tortured in 1987 and their bodies blown up.
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