The Presidency announced in a statement on Thursday that the appointment was made in terms of section 193(4) of the Constitution, and on the recommendation of the National Assembly.
Zuma also thanked outgoing Public Protector, Advocate Thulisile Madonsela for her services and wished Advocate Mkhwebane all the best in the execution of her new responsibilities.
Mkhwebane was selected from over 60 candidates nominated by South Africans. They included judges Siraj Desai and Sharise Weiner, Prof Bongani Majola, and advocate Muvhango Lukhaimane.
Her candidacy was endorsed with an overwhelming 263 votes during a debate in the National Assembly on September 7. A total of 79 MPs voted against it, while 1 MP abstained.
Only the Democratic Alliance opposed her nomination and accused her of being a spy on the State Security Agency’s payroll.
Meanwhile, Zuma is on Thursday expected to meet with Madonsela to answer her questions about the Gupta family’s alleged influence on Cabinet decisions.
Madonsela started her probe into allegations of state capture in March, after the Catholic Dominican Order asked her to investigate.
She is trying to conclude her preliminary report into state capture before leaving office on October 14. She had said she was in a race against time.