Previously, the Scottish Government offered a masters degree scholarship to poorer women in Pakistan and a separate programme for disadvantaged and minority children.
Now, the new scheme will provide scholarships to women and girls through their secondary education, undergraduate degree and masters degree.
Pakistan has 25 million children who do not go to school and more than half of them (55%) are girls, according to a Scottish Government report published last year.
For the poorest 20%, two in three girls do not attend school, due to factors such as discrimination, conservatism and lack of facilities and teachers.
The First Minister attended the annual dinner organised by homelessness campaigners Social Bite in Edinburgh on Wednesday evening where Ms Yousafzai, the youngest Nobel Prize laureate, was a guest speaker.
Ms Yousafzai became an activist for female education after being shot by the Taliban.
The First Minister said: “Tackling poverty and inequality is a central aim of the Scottish Government, whether that is at home or abroad and girls still face the largest barriers to accessing secondary and undergraduate education.
“In 2013 we set up a masters scholarship scheme for Pakistani women which was inspired by Malala Yousafzai’s courageous campaign for better education for girls.
“The Scotland-Pakistan Scholarship for Young Women and Girls will help a new generation of Pakistani women and girls achieve their full potential and ambitions.”
The previous scholarship helped more than 500 women between 2013 and 2016.
More than 5,600 women applied in 2017/18 and 173 scholarships were awarded.
The children’s scholarship programme helped more than 4,000 children complete a year of schooling, 2,000 of which were in 2017/18.