In his second reshuffle this year, Zuma dropped Higher Education minister Blade Nzimande, a member of the South African Communist Party, which is a key political ally of the ruling ANC.
Zuma also moved State Security Minister David Mahlobo to the energy portfolio, the president’s office announced, reviving debate over controversial and costly plans for nuclear energy.
Nzimande has in recent months been incessantly vocal in calling for Zuma to go.
“The ANC is being stolen in broad daylight,” Nzimande told an anti-graft strike last month which urged Zuma to quit over a series of corruption scandals.
The SACP and the country’s largest trade union, COSATU, are long-term political allies with Zuma’s African National Congress (ANC) party.
Both the SACP and COSATU have endorsed Cyril Ramaphosa as the ANC’s new president.
Zuma is backing his ex-wife Nkosazana Dlamini-Zuma to succeed him.
The ANC is due to elect Zuma’s successor as party leader in December, ahead of general elections in 2019.