According to a letter from Minister Neda Mohammad Nadeem sent to the country's authorities and private universities, the Taliban regime now bans women from studying at universities.
"You are all informed to implement the said order to suspend the education of women," the minister writes in the letter.
The decision shall enter into force immediately and apply indefinitely.
Most teenage girls in Afghanistan have not set foot in a school since the Taliban took power last August.
Initially, younger girls could go to school, but since March this year only a few schools for girls have been able to stay open.
Women's rights are curtailed
As recently as two weeks ago, however, the Taliban announced that girls in 31 of the country's 34 provinces would be allowed to take a matriculation exam, despite being banned from classrooms.
The Taliban had then indicated that those who pass the matriculation exam can apply for higher studies.
Since the Taliban took power, women's rights have been tightened step by step.
Women have been forced to wear full-coverage clothing and banned from parks, gyms and theme parks.
They are also not allowed to travel long distances without a male companion.
Many have been forced to stop gainful employment.