"Names have meaning and symbolic values. Public spaces and even private buildings are given names to celebrate the achievements of people, or to honour the legacies they have left behind for communities," he said.
The Pretoria Academic Hospital was renamed the Steve Biko Academic Hospital.
The Coronation Hospital in Johannesburg would become the Rahima Moosa Mother and Child Hospital.
Johannesburg General Hospital was renamed the Charlotte Maxeke Johannesburg Academic hospital.
Hlongwa said a lengthy and exhaustive process had been followed since August 2007 to enable the name changes. He spoke of changes allowing a clean break with a past that "no right-minded person can be proud of".
He said the process to select the new names was not a-historical and the three names selected were from three eras in South African politics.
Charlotte Maxeke was selected to characterise the early 20th century, which saw the rise of resistance movements, including the ANC.
Rahima Moosa was selected to represent the 1950s when she took part in the passive resistance movement, and was one of the four women who led the 1956 women's march to the Union Buildings.
Steve Biko was selected to represent the 1970s which saw the Soweto uprising. Hlongwa described it as a time "when the internal resistance against the [apartheid] regime gained overwhelming popular support and international recognition".
The changes would be official as of Monday, he said.
Hlongwa said the name changes would enable people to identify with the institutions that they used, as well as honouring prominent figures in South Africa's history.
The Gauteng Democratic Alliance however said that their objections to the name changes had been brushed aside.
"There really should have been more public participation in the naming of these hospitals. Public hearings should have been held at the hospitals, instead of a closed process by a panel appointed by the department," said DA health spokesperson Jack Bloom.
The department should rather have considered the names for new hospitals being built in Vosloorus and Jabulani as well as the hospitals that had been planned for Diepsloot, Daveyton, Kruisfontein and Lenasia, Bloom said.