Pupils attending Hoërskool Pretoria West will not be allowed to wear skinny pants despite their outburst last week.
"As parents we must always take charge of our children's behaviour and empower educators to instil necessary discipline to learners," Gauteng Education MEC Panyaza Lesufi said.
"The day we allow ill-discipline to prevail in our schools, we will all be doomed. Ill-discipline must not be tolerated in our schooling environment."
Parents and the school's governing body voted against the proposed amendment to the school's code of conduct on Thursday.
Last week, pupils protesting at the high school boycotted classes and demanded to be allowed to wear skinny pants, except for the matriculants who were preparing for their preliminary exams. At the time, SGB chairperson Brian Zyster said the protest was started by problematic pupils.
"My worry is that the ringleaders are students who were suspended two weeks ago, and the worry now is that the ringleaders are using this thing to destabilize the school," said Zyster.
The department has assured parents that teaching and learning would continue unhindered and asked learners not to disrupt schooling because it would impact negatively on their future.
The department also urged learners to use proper channels to raise their grievances in order to eliminate protests and disruptions.