One by-election would be held in each province, the IEC said in a statement.
In the Free State Ward Nine in the Dihlabeng municipality (Bethlehem) would be contested by the African National Congress, Democratic Alliance, Economic Freedom Fighters, and Freedom Front Plus.
The ward's ANC councillor resigned.
In Gauteng, Ward 68 in Johannesburg will be contested by independent candidate Patrick Luvuyo Jafta, the ANC, DA and African Independent Congress.
The ward's DA councillor resigned.
Source: Sapa