A native of the Transkei, she grew up in a township near Cape Town, where she worked as a domestic and completed her secondary education by correspondence. Magona later graduated from the University of South Africa and earned a graduate degree from Columbia University.

She published her autobiography To My Children's Children in 1990. In 1998, she published Mother to Mother, a fictionalized account of the Amy Biehl killing, which she adapted to a play. This was performed at the Baxter Theatre complex in late 2009 and the film rights to the novel were acquired by Type A Films. She has also written autobiographies and short story collections. Her novel Beauty's Gift was shortlisted for the Commonwealth Writers' Prize (Africa). She retired from the United Nations in 2003 and currently lives in South Africa.

In 2009, Please, Take Photographs, her first collection of poems, was published by Modjaji Books.