President Jacob Zuma, in a statement from the presidency, thanked outgoing Public Protector Advocate Thulisile Madonsela for her service and wished Mkhwebane well.
Earlier, parliament recommended her appointment.
The National Assembly approved the appointment of Mkhwebane amid objections from the Democratic Alliance that her stint as an analyst at the State Security Agency made her an unsuitable and suspicious choice for the job.
The Congress of the People abstained from the vote, concurring that her CV left unanswered questions.
Her nomination was approved by 263 to 79 votes and one abstention.
Mkwebane was nominated by the Inkatha Freedom Party. She emerged as the favourite for the ANC and remaining opposition parties to succeed Thuli Madonsela on a shortlist full of legal professionals after the perceived choice of the ruling party Judge Siraj Desai lost his temper during an interview for the post, leading opposition parties to plead that he lacked the cool to withstand the pressures of the job.
DA MP Glynnis Breytenbach said the support for Mkhwebane was unreasonable as she had “little or no experience to justify such an appointment” and said her decision to leave a senior post at the department of home affairs earlier this year to join the intelligence service bode ill in a climate where the president was seen as abusing state agencies.
“The ineluctable conclusion is simply that she is on the payroll of the SSA [State Security Agency],” Breytenbach said.
But the Economic Freedom Fighters’ (EFF) deputy leader Floyd Shivambu said his party saw her as the best candidate with the best strategy to expand the reach of the chapter nine institution to far-flung rural areas to fight corruption and ensure the poor were not robbed of basic services.
Given Mkhwebane’s past experience — she worked for the Public Protector’s office for five years — Shivambu said she should be able to “hit the ground running”, adding that the EFF was particularly impressed with her view on the independence of the institution.
She expounded the view that the Public Protector was accountable only to the Constitution, though administratively it reported to Parliament. It is a view that was firmly held by Madonsela, and lead to bitter clashes with Parliament’s portfolio committee on justice.
Shivambu paid unstinting tribute to Madonsela, saying her often lonely battles ended in vindication and made her “the true biblical David”. He proposed that the National Assembly invite her to give a farewell address when she leaves the office in October.
Nqabayomzi Kwankwa from the United Democratic Movement said it would be unfair to disqualify Mkhwebane on the basis of a very brief stint at the SSA, and noted that it was a state intelligence service and ideally the “state is an inclusive concept”.
Steve Swart from the African Christian Democratic Party agreed, and argued that she had emerged as the consensus candidate that found the widest support across parties in the selection process, which last month saw a marathon process of 14 shortlisted candidates interviewed in a day that ran into the early hours of the next.
In media reports on Tuesday, Mkhwebane said she did not see the need to respond to the DA’s allegations, except to say that the official opposition had been party to the selection process and had all necessary information about her career.