Development Minister Svenja Schulze backed a freeze after what she called an “irresponsible attack on aid to the Afghan people”.
It came as a German food and hygiene agency became the latest NGO to say it could not continue with its usual operations in Afghanistan.
Mathias Mogge, head of the agency World Hunger Aid, said the ban would have “catastrophic effects” on food, health and education programmes.
An order issued by the Taliban on Saturday banned women from going to work at aid agencies in Afghanistan.
The order came days after women were banned from Afghan universities in another move condemned by western powers.
“Without female staff, organisations cannot continue their work for half the population in many areas,” Germany's Ms Schulze said in a statement.
“This has entirely changed the circumstances. I therefore support suspending the support that we currently provide along with others.”
Ms Schulze said she would call a meeting with the World Bank and donors to discuss “how and whether support for the Afghan people can be continued in the circumstances created by the Taliban”.
The EU's top diplomat, Josep Borrell, separately warned that member states could scale back their assistance to Afghanistan.
Europe “will have to consider what consequences this decision, and the recent decision by the Taliban to close universities for women, will have,” he said.
Several aid groups including Save the Children have announced they are pausing their humanitarian work.
The UN says millions of Afghans are in need of humanitarian assistance.
A joint statement from 183 NGOs said the Taliban's ban would affect food distribution, health provision, education and disability services.
It said women made up more than a quarter of the 55,000 Afghan nationals employed by those agencies.
Mr Mogge, from the German food agency, called on the international community to negotiate a reversal of the ban.
The group “respects the traditional, cultural and religious values of the country, but we categorically reject any discrimination on the basis of gender, religion age or ethnic background,” he said.
“Without our female colleagues we can no longer adequately provide for women and girls in the country.”
Aid agencies face having their licences suspended in Afghanistan if they do not comply with the ban on women.
The Taliban tried to justify the move by saying complaints had been made about the dress code of female aid workers.
French Foreign Minister Catherine Colonna said the ban was the latest example of a “systematic exclusion of women” since the Taliban returned to power in August 2021.
Western powers said at the time that any engagement with the Taliban would depend on them respecting women's rights, combating terrorism and allowing people to leave.
However, the past 16 months have seen the Taliban enforce a strict dress code and ban girls from attending secondary school.
The militants have also been accused of flouting their promise to tackle terrorism, after Al Qaeda leader Ayman Al Zawahiri was tracked down and killed in Kabul.