During the apartheid era, it was designated the "whites only" school.
In a statementissued on Tuesday, Gauteng Department of Education stated that during a visit by Panyaza Lesufi, the province's education minister, it had learned of allegations of racist abuse of black students on the basis of their hair and their speaking in African languages.
Learners also raised concerns over not being allowed to wear hairstyles such as Afros.
After the girls marched in protest at the school Friday, their cause drew widespread support on social media, under the hashtag #StopRacismAtPretoriaGirlsHigh.
Pretoria Girls High was founded in 1902 as a multi-racial school, according to its website, but was a whites-only institution during the apartheid era.
"When her parents fought the suspension, they used the school's hair regulations against her", Lokotwayo wrote, adding "She represents everything that is lovely about this country".
Lesufi told Cape Talk students informed him of some especially racist practices teachers use to discourage natural hair.
The girls will also receive psychological counseling to assist with the trauma they have suffered and that the school must ensure that good performance must continue as they have done in their National Senior Certificate examination. "She'd get home and cry because of how she was treated because of her hair, and say that the school said her hair is a distraction and called it exotic", said Amira Patel, the older sister of 13-year-old Zulaikha Patel.
"It ends here. If there is someone who needs to pack their bags and leave this school, then they will", he said. "The constant policing of the clothing, hair, bodies and behavior of women of color takes its toll on the psyche of young girls, who must begin to unlearn and recover from their education in the tertiary sector".
"This is disturbing because the girls are very traumatised".
The DeKalb County School System confirmed it has taken disciplinary action against two students who were accused of setting a classmate's hair on fire.
One of the teachers even threatened her with detention if the hair was not "fixed" and said that she would remain in detention until she changed her hairstyle.
"That is not fair because some pupils have natural (ly curly) hair so we have agreed with the student governing body that it be suspended", he said.
"It was odd. We've never had security at assembly before", the pupil said. "Why do black girls always receive the shortest end of the stick?"