Afghan universities will be segregated by gender, and a new Islamic dress code will be introduced, the Taliban said.
Higher Education Minister Abdul Baqi Haqqani has indicated that women will be allowed to study, but not on the side of men.
He also announced a review of the curriculum.
Women and girls were banned from schools and universities under the Taliban regime between 1996 and 2001.
The Taliban have said they will not prevent women from studying or getting jobs. But since taking office on August 15, they have asked all women, except those in the public health sector, not to go to work, until the security situation improves.
Sunday's announcement of higher education policy comes a day after the Taliban hoisted their flag over the presidential palace, marking the beginning of their rule. They took over the reins of government elected last month.
The policy reflects a major shift from the accepted approach before the Taliban takeover. Universities studied collaboratively, men and women studying together, and female students did not have to adhere to the dress code.
But Mr Haqqani did not apologize for ending the combined classes. "We have no problem ending a mixed education system," he said. "People are Muslims and they will accept it."
Some have suggested that the new rules will exclude women from education because universities do not have the resources to provide separate classes. However, Mr Haqqani emphasized that there were enough female teachers and that in their absence alternatives would be found.
"It all depends on how the university works," he said. "We can also use male teachers to teach behind the curtain, or we can use technology."
Girls and boys will also be segregated from primary and secondary schools, which were already common throughout Afghanistan.
Women will be required to wear hijabs, however Mr Haqqani did not specify if additional concealment would be required.