The proceeds will be donated from her Malala Fund to a special fund designed to assist local NGOs working to educate girls and women in Nigeria, where more than 200 schoolgirls are missing after being snatched at gun point last month by extremists.
Auction house Christie's had estimated the portrait of the veiled teenager -- done in 2013 by leading British artist Jonathan Yeo -- would fetch $60,000-$80,000.
But after several bids it was snapped up in just a few minutes at a higher price.
Malala, now 16, was shot by a Taliban gunman in 2012 over her outspoken views on education for girls in her home region of northwest Pakistan. After undergoing extensive medical treatment, she now lives in Britain.