Gauteng Education MEC Panyaza Lesufi approved the renaming of Höerskool HF Verwoerd in Pretoria to Rietondale Secondary School on Monday.
"My mission in this world is to reverse everything this man called Verwoerd has done to our education system. Others names like Jan Smuts will also fall," Lesufi tweeted on Monday evening.
Verwoerd, who was leader of the apartheid National Party, served as prime minister of the country from 1958 until 1961.
The man, who was dubbed the "architect of apartheid", introduced the system of Bantu Education.
"There is no place for [the Bantu] in the European community above the level of certain forms of labour... What is the use of teaching the Bantu child mathematics when it cannot use it in practice?" Verwoerd, who was Minister of Native Affairs at the time, stated at the time.
Gauteng Department of Education spokesperson Steve Mabona confirmed the school's name change to News24 on Tuesday.
"We are not targeting any schools. This process was initiated by the school community, parent body etc. which led to a process observed by the District Office which involved consultation.
"These are the architects of apartheid and the school community decided that they did not want to be associated with that name. It is an initiative from the parent body because they want to contribute to social cohesion and non-racialism," Mabona said.
Lesufi's tweet comes a day after lobby group Afriforum accused Lesufi "a serious invasion of Afrikaans speakers' dignity".
AfriForum said that Lesufi had said that it was "beyond his comprehension" why the battle for Afrikaans education still continued and that the insistence on it would "cause Afrikaans children damage".
"Lesufi's depreciatory attitude concerning Afrikaans and Afrikaans speakers is displayed by his point of view that Afrikaans isn't worth fighting for and that the speakers of the language will be hampered if they insist on their mother tongue.
"Lesufi is pretending to be a protagonist against racism, but simultaneously doesn't hesitate to express offensive utterances towards the Afrikaans speaking section of the population," AfriForum CEO Kallie Kriel said in a statement on Monday.