President Mamnoon Hussain termed Chinoy's choice of the subject as "heroic".
"Sharmeen had performed a heroic deed by highlighting an important social issue. She deserves congratulation for this," Hussain said.
Chinoy, 37, was today awarded the Oscar for the documentary "A Girl in the River: The Price of Forgiveness" which tells the story of a girl who was shot in the face and thrown in a river for marrying a man of her choice.
"Every year, more than 1,000 girls and women are the victims of religiously motivated honour killings in Pakistan, especially in rural areas," the Oscars website said.
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Special Assistant to the Prime Minister on Foreign Affairs (SAPM) Syed Tariq Fatemi also congratulated Chinoy for winning the best documentary short award at the 88th Academy Awards at a ceremony held at Los Angles, United States.
"It was a matter of pride for the nation that a daughter of Pakistan had yet again, achieved this distinction, which was a source of inspiration for all Pakistani women," he said.
Earlier, Prime Minister Nawaz Sharif congratulated her for the Oscar nomination and also organised a special screening of her documentary at his office exactly a week ago.
Sharif said on the occasion that "there was no honour in honour killing" and reiterated his government's unequivocal resolve to ensure women's rightful place in society, as well as to bring an end to violence against women.
This is the second win for Chinoy, who previously bagged the Oscar in the same category in 2012 for "Saving Face", a documentary which dealt with another important issue of acid throwing on women in Pakistan.