"This decision follows the recent announcement by the Taliban of further restrictions on women's and girls' education and employment opportunities and their ability to access parks and gyms," it said in a statement.
"CA is committed to supporting growing the game for women and men around the world, including in Afghanistan.
"(We) will continue to engage with the Afghanistan Cricket Board in anticipation of improved conditions for women and girls in the country," it added while thanking Canberra for its support.
Australia will forfeit 30 competition points for the series, which go towards World Cup qualification. But they have already secured automatic qualification to the 50-over tournament in India in October.
The Taliban regained control of the Asian nation in mid-2021 and immediately placed restrictions on female participation in sport.
The hardline Islamists have also barred teenage girls from secondary schools and last month banned women from attending universities, prompting global outrage.
More recently, women were told they could no longer work in Afghanistan's aid sector.
Females have also been pushed out of many government jobs, prevented from travelling without a male relative, and ordered to cover up outside the home, ideally with a burqa.