The 15-year-old pupil later died by suicide.
The university confirmed the teacher would continue with her studies, pending the finalisation of the investigation.
On Tuesday, its spokesperson, Louis Jacobs, said the university had written to the higher education minister informing them it was aware of the incident and had commenced with the investigation.
Teacher Called Learner Sissy Boy
Tiro Moalusi, a Grade 9 PJ Simelane Secondary School pupil, died by suicide a month ago after the student teacher allegedly mocked him in front of his peers for being gay.
It is alleged she called him “ngwanyana abuti” (sissy boy), prompting her and the whole class to laugh. When he confronted the student teacher and told her how it made him feel, she allegedly continued to laugh.
Jacobs said the university had since identified her as a third-year student who was enrolled at the faculty of education.
He added the student teacher was doing her practical at the school when the incident occurred.
South Africa has a constitution forbidding discrimination on the grounds of sexual orientation.
