He said the prisoners, all from the Eastern Cape and reportedly mostly African National Congress and Pan Africanist Congress members, had been petitioning the government for "some years".
"These are people who are in jail as a result of activities that were conducted in the struggle for our liberation," he told journalists at Tuynhuys on Wednesday.
Justice Minister Penuell Maduna had been considering the matter for quite some time, and having looked into it, recommended that the "amnesties" be granted.
"It's a group of people who petitioned the government on the basis that they were involved in the struggle, and the reason they are in jail is as a result directly of those activities," Mbeki said.
He said if any other requests for pardon were made, they would be dealt with "on the basis of whatever approaches are made".
Vigilantes convicted for mob killings
He did not know whether any other approaches would be made.
Mbeki's statements appear to fly in the face of justice ministry claims that the pardons were not politically motivated.
Although the government has refused to release the names of the 33, it has been reported that they include former Ciskei strongman Kwane Sebe, a as well as vigilantes convicted for mob killings.
Among them are men who were refused amnesty by the Truth and Reconciliation Commission on the basis that their deeds had no political motivation.
The justice ministry says releasing their names could jeopardise their safety.
Justice spokesperson Paul Setsetse said earlier this week that he saw no reason why the amnesties had become "such an issue".
"Prisoners are released daily by a parole board, on the discretion of correctional services or on completion of sentences and their names are not published.
"So we see no reason why these (the 33 prisoners) should be an issue," he said.
He said amnesty applications were handled by civil servants without any consideration of an applicant's political status.