Vavi was speaking at the opening of the Equal Education national summit in Tembisa, north of Kempton Park.
"After 18 years of democracy, our education system still reproduces both racial and class inequalities over and over again...the struggle for the transformation of education and training is far from over," said Vavi.
He said similar inequalities were seen in health care, public transport, housing and all basic services.
Vavi said the textbook scandal in Limpopo was a sign that the education system in the country was dysfunctional.
"Only seven per cent of schools have libraries, only five per cent have stocked science laboratories and just one per cent of the schools have internet access," he said.
He said if the children of politicians and business people had been affected by the textbook scandal in that province, the matter would have been dealt with speedily.
"In fact the entire education system would have long undergone significant change for the better."
Vavi said all those who had the power to be "heard" should be ashamed that there was a large gap between leaders and those that have placed them in power.
"As the general secretary of more than two million workers across the length and breadth of this country, I offer our unconditional apology to the affected children and parents."
He said for the education to improve in the country, teachers, parents, governing bodies and government officials had to change their mind-sets.
"We must wage a war on the kind of gross incompetence we witnessed in Limpopo and in many other provinces. If officials are not doing their job their heads must roll.
"We cannot tolerate a culture of mediocrity, and mortgaging our children's future."
Darul Ihsan Media Desk