De Klerk said Thatcher did not give the "slightest support for apartheid or for racial discrimination of any kind".
In life, and after her death last week, Thatcher was accused of racism because of her opposition to sanctions against the apartheid regime.
De Klerk said she simply understood the politics at play better than most contemporaries.
"Thatcher understood that sanctions have limited effect on states that believe that their very existence is at stake," said De Klerk, who will attend the "Iron Lady's" funeral.
De Klerk said he consulted with Thatcher during the dying year of apartheid, to inform her about his "intention of embarking on fundamental constitutional transformation".
De Klerk's support is unlikely to sway opinion about the polarising British premier.
Last week the African National Congress greeted Thatcher's death with mixed feelings, recalling her hostility towards the party she once described as a terrorist organisation.
The ANC expressed "sadness" while noting that Thatcher "redefined British politics and public administration".
The only hint of lingering resentment was an acknowledgement that "the ANC was on the receiving end of her policy".
Thatcher died on 8 April aged 87 after suffering a stroke.
