The Scottish Government is putting up £300,000 for the initiative, with External Affairs Minister Humza Yousaf saying it would help these females "achieve their potential and ambitions".
The scholarship was inspired by 16-year-old Malala Yousafzai, who was shot in the head while travelling on a school bus in Pakistan last October after her outspoken views on education and women's rights angered the Taliban.
More than seven million children in Pakistan do not attend school, with girls much more likely than boys to miss out on an education.
The two-year Masters scholarship scheme announced by the Scottish Government will help around 30 to 40 young Pakistani women from disadvantaged backgrounds to go to university, and will cover their university fees as well as assisting with living expenses and travel costs
Mr Yousaf said: "Education is a fundamental human right and one that we take for granted in Scotland where our excellent education system is free and open to all.
"These scholarships will help disadvantaged women in Pakistan get the financial support needed to complete their studies, secure a more prosperous future and better support their families and communities."
He added: "They have been inspired by Malala Yousafzai, the schoolgirl shot by the Taliban in northern Pakistan and her courage in taking a stand on girls' education. Through the story of Malala, many people in Scotland have become aware of some of the challenges that many women in Pakistan face in securing an education.
"It is through education that girls and women can gain the freedom to make choices, shape their future and build more inclusive and just societies. The more education a girl has, the less likely she is to die in childbirth, and the more likely she is to be able to provide adequately for herself and her family."
The minister continued: "Although much progress has been made in the last 20 years there is still much to do with one in four adults in the developing world being illiterate and over seven million children in Pakistan not getting access to education.
"Girls' education is especially important. The statistics show that around half of girls in the world's poorest countries still have no access to primary education, and the percentage of girls attending secondary schools and universities is considerably lower.
"I am delighted that we are playing a part in helping these women achieve their potential and ambitions, helping to build a secure future for themselves and their families."
The initiative was unveiled the day after Malala was reunited with two school friends injured in the same attack during a visit to Scotland yesterday.
Malala addressed the first public meeting of the Global Citizenship Commission at Edinburgh University, telling them: "We are not afraid and now people are supporting us and that is the greatest courage, and that is the weapon that we have got, the unity and togetherness."