The portrait of Bibi Aisha by Jodi Bieber, which appeared on the cover of the August edition of the magazine, was also awarded first prize in the Portraits Singles category.
Aisha, an 18-year-old woman from Afghanistan, had her ears and nose cut off, reportedly under the instructions of the Taliban after she had tried to flee an arranged marriage. She was later rescued by US military aid workers and now lives in the US.
According to a release from the World Press Photo (WPP) organisation, Bieber has previously won eight WPP awards and is the second South African photographer to win the highest honour in the contest.
"This could become one of those pictures - and we have maybe just ten in our lifetime - where if somebody says "you know, that picture of a girl...", you know exactly which one they're talking about," jury chair David Burnett said in the release.
"It's an incredibly strong image," juror Ruth Eichhorn added. "It sends out an enormously powerful message to the world, about the 50 per cent of the population that are women, so many of whom still live in miserable conditions, suffering violence. It is strong because the woman looks so dignified, iconic."
The jury gave prizes across nine themed categories to a total of 56 photographers from across the world, including Australia, Brazil, China and France.
This year's contest saw a record number of images submitted, 108,059 in total, with just under 6,000 participating photographers representing 125 nationalities.
Bieber will receive her award, a cash prize of €10,000, during a ceremony in Amsterdam on 7 May, along with a Canon EOS Digital SLR Camera and lens kit, donated by Canon.
An exhibition of the prize-winning photography from the contest will be shown at Amsterdam's the Oude Kerk [Old Church] from 22 April to 19 June and will then visit more than 100 locations around the world.
Image of Bibi Aisha courtesy of World Press Photo.
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