The "Malala Fund for Girls' Right to Education" aims at raising billions of dollars to ensure that all girls go to school by 2015 in line with United Nations Millennium goals.
Pakistan Education Minister Waqas Akram signed the agreement with the United Nations Educational, Scientific and Cultural Organization head Irina Bokova.
"A young determined daughter of my country was attacked by the forces of darkness," Zardari said at the high-profile "Stand Up For Malala" event at the UNESCO headquarters in Paris.
"We are facing two forces in the country; Malala represents the forces of peace and we are fighting with the forces of darkness, hatred and violence," he said.
The ceremony drew French Prime Minister Jean-Marc Ayrault, former British premier Gordon Brown, the UN Special Envoy for Global Education, and the former presidents of Finland and Chile.
UN Secretary General Ban Ki-moon, US Secretary of State Hillary Clinton and the EU's top diplomat Catherine Ashton send special videotaped messages of support.
The 15-year-old schoolgirl, who is recovering in a British hospital after being brutally attacked on her school bus on October 9, will herself join the campaign when she is better.
Ziauddin Yousafzai, Malala's father, a former teacher and headmaster has been appointed to help in what Brown has dubbed a new 'Malala Plan' to get all girls into school around the world by the end of 2015.
Zardari slammed Islamic fundamentalists for giving the religion a bad name.
"The first word of the holy Koran is 'iqra' which is read," he said, attacking the "fringe minority of darkness, of hatred, of conflict.
"What extremists fear is a girl with a book in her hand," he said.
The UN estimates that 61 million children do not go to school and girls account for two-thirds of this number.
In an attack that shocked the world, Malala was shot in the head as punishment for the "crime" of campaigning for girls' rights to go to school.
She survived the murder attempt but requires reconstructive surgery after the bullet grazed her brain, coming within centimetres of killing her.
Brown said the initiative, which he hoped would attract "billions of dollars of public subscriptions", also aimed at stopping social evils such as child marriage and violence against girls.
He said he wanted Malala's birthday, July 12th, to be designated a day of action each year when children around the world are invited to march, demonstrate, petition and pray for education to be delivered worldwide.
Clinton highlighted the pressing need for universal education, saying: "Closing the education gap is a powerful prescription for economic growth."
Ashton said the EU, which on Monday collected this year's Nobel Peace Prize said the estimated 930,000-euro ($1.2 million) prize money would be donated to help children affected by war.