Mbeki died in hospital where she was admitted two weeks ago with a chest infection and heart problem.
President Jacob Zuma's office described her as a "consummate activist ... who dedicated her life and that of her family to the struggle for liberation in South Africa from an early age."
She "was fiercely outspoken on political and socio-economic issues till the end," it said in a statement.
Mbeki was the mother of South Africa's second post apartheid leader, who took over from Nelson Mandela in 1999.
Her husband was Govan Mbeki, a late stalwart of the African National Congress and South African Communist Party.