Describing the move as deeply shocking, ministry spokeswoman, Anne-Claire Legendre added: "This decision adds to the list of countless violations and restrictions on the rights and fundamental freedoms of Afghan women pronounced by the Taliban.
"France recalls its constant commitment in favour of a universal right to education and its particular attention to the defence of the rights of girls, adolescents and women."
Hundreds of young women were stopped by armed guards on Wednesday from entering Afghan university campuses, a day after the Taliban's announcement.
"You all are informed to immediately implement the mentioned order of suspending education of females until further notice," Neda Mohammad Nadeem, the Minister for Higher Education said in a statement.
Despite promising a softer rule when they seized power in August last year, the government have ratcheted up restrictions on all aspects of women's lives, ignoring international outrage.
The US Secretary of State, Antony Blinken, added: "The Taliban cannot expect to be a legitimate member of the international community until they respect the rights of all in Afghanistan. This decision will come with consequences for the Taliban."
The international community has made the right to education for all women a sticking point in negotiations over aid and recognition of the Taliban regime since the takeover.
The British Prime Minister, Rishi Sunak, said that banning women from university was a grave step backwards.
"The women of Afghanistan have so much to offer," Sunak tweeted. "We will judge the Taliban by their actions".
UN Secretary-General Antonio Guterres, meanwhile, was deeply alarmed, his spokesman said Tuesday.
"The secretary-general reiterates that the denial of education not only violates the equal rights of women and girls, but will have a devastating impact on the country's future," Stephane Dujarric said in a statement.
In the 20 years between the Taliban's two reigns, girls were allowed to go to school and women were able to seek employment in all sectors, though the country remained socially conservative.
The ban on higher education comes less than three months after thousands of girls and women were allowed to sit for university entrance exams across the country, with many aspiring to choose teaching and medicine as future careers.
Most teenage girls across the country have already been banned from secondary school, severely limiting university intake anyway.
After the Taliban takeover last year, universities were forced to implement new rules including gender-segregated classrooms and entrances, while women were only permitted to be taught by professors of the same sex, or old men.
The Taliban adhere to an austere version of Islam, with the movement's supreme leader Hibatullah Akhundzada and his inner circle of clerics against modern education, especially for girls and women.
But they are at odds with many officials in Kabul - and among their rank and file - who had hoped girls would be allowed to continue learning following the takeover.
In a U-turn, the Taliban in March blocked girls from returning to secondary schools on the morning they were supposed to reopen.
Several Taliban officials maintained the secondary education ban was only temporary, but have made excuses for the closure - from a lack of funds to the time needed to remodel the syllabus along Islamic lines.
Since the ban, many teenage girls have been married off early - often to much older men of their father's choice.
Several families interviewed by the French news agency AFP last month said that, coupled with economic pressure, the school ban meant that securing their daughters' future through marriage was better than them sitting idle at home.
Women have also been pushed out of many government jobs - or are being paid a pittance of their former salary to stay at home.
They are also barred from travelling without a male relative and must cover up outside of the home, ideally with a burqa.
In November, women were prohibited from going to parks, funfairs, gyms and public baths.
The authorities have also returned to public floggings and executions of men and women in recent weeks as they implement an extreme interpretation of Islamic sharia law.