Women and girls are barred from public and private universities "until further notice", a statement from the Taliban-led Ministry of Higher Education said.
The decision is to come into effect immediately.
It is likely to prompt outrage from rights groups and the international community, which has not officially recognised the Taliban's administration since the group's rapid takeover of Afghanistan last year, following a precipitous withdrawal of international forces.
Millions of girls are barred from attending school under rules enforced by the Taliban. While girls in primary school are generally allowed to attend classes, restrictions remain and vary from province to province.
Women and girls have held protests across the country, demanding they be let back into the classroom.
Taliban authorities sparked anger this month after saying girls barred from school for almost a year could now take exams — a decree dismissed as "meaningless" by Afghan pupils.
The latest decision is another sign the Taliban is tightening restrictions on Afghanistan's millions of female adults and children after hollow public claims its takeover would not affect women's rights.
"Afghanistan now officially becomes a living hell on Earth for women and girls," Afghan activist and journalist Nilofar Ayoubi wrote on Twitter.
The decision is the "final nail in the coffin", said journalist Deepa Parent.
The Taliban have continued to exclude women from public life, barring them from parks and hammams this month. They have also resumed executions and public floggings, sparking fears of a return to their iron-fist rule of the 1990s.
Girls' schools that have stayed open have been targeted by extremists.
In September, at least 35 people — mostly women — were killed in a suicide bombing as they prepared for university entrance exams in the Dasht-e-Barchi neighbourhood of Kabul.
Six people were killed at a high school in the same neighbourhood in April, and in May last year a bombing killed 85 at a girls' school.