Those who confessed to the commission could seek amnesty for their crimes, but some chose not to.
Vlok appeared before the commission and admitted his role in a series of bombings but did not seek amnesty for the 1989 attack on Reverend Frank Chikane, now an adviser to Thabo Mbeke, the president.
The two men have recently made peace.
Last September, Vlok even washed Chikane's feet in an act of contrition seen as hugely symbolic in a country where many people consider themselves to be devout Christians.
|Protesters outside court demanded that Vlok |
face trial for other alleged abuses [EPA]
But while Chikane said he had has forgiven Vlok, he said he could not stop the court process.
Many feel that Vlok, who was security minister from 1986-1989, when an estimated 30,000 people were detained, should not be standing trial.
Antjie Krog, an author and academic, said: "I feel they should have focused on the people who didn't participate in the [reconciliation] process, instead of going for a soft target. What kind of message are you sending, 'if you came forward it will just continue'?"
But others say the trial should been seen as another step towards reconciliation.
Zweli Mkhize, who says he was tortured by the white security forces, said: "Vlok and his like must face justice for the atrocities. How can there be reconciliation when there is no justice?"
Vlok's trial had also been expected turn the spotlight on de Klerk, who became president in 1989 and helped usher in black majority rule.
De Klerk said he knew nothing of any atrocities and that if there were to be any further prosecutions, former ANC fighters should be brought to book along with members of the white security forces.
Although the vast majority of atrocities were committed by white security forces, ANC guerrilla forces waged landmine and bombing campaigns in which civilians died.
Among those were Kobie van Eck and her two children, aged two and eight, who died with three of their friends when their vehicle hit a mine laid by the ANC's military wing in 1985.
The two men involved were sentenced to life imprisonment but then given an amnesty by the Truth and Reconciliation Commission.
Dirk van Eck, who survived the attack, is now lobbying for the ANC leaders who authorised the land mine campaign to be brought to justice.