Jonathan Torgovnik, 38, photographed Joseline Ingabire with her two children, both born during the Rwandan conflict.
Ms Ingabire is pictured embracing her second daughter, Leah Batamuliza, while her first daughter Hossiana is in the background in front of their mud-walled home.
The militia murdered Ms Ingabire’s husband in front of her when she was two months pregnant with their daughter Hossiana.
Ms Ingabire was raped repeatedly throughout her first pregnancy, even at nine months, and after she gave birth to Hossiana. She eventually became pregnant with her second daughter and infected with HIV.
The portrait — entitled Joseline Ingabire With Her Daughter, Leah Batamuliza, Rwanda — was taken after Mr Torgovnik interviewed her about her experiences.
Mr Torgovnik, a former combat photographer in the Israeli army, took the photograph as part of his series, Intended Consequences: Mothers Of Genocide, Children Of Rape.
The ongoing project documents the lives of Tutsi women raped during the 1994 Rwandan genocide.
A total of 2,700 photographers from around the world entered 6,900 submissions for the National Portrait Gallery prize.
Mr Torgovnik was presented with a £12,000 cheque at a ceremony on Tuesday.
Meanwhile, Irishman Ivor Prickett, 24, won the inaugural Godfrey Argent award for a picture from a series on Serbian families returning to Croatia after being displaced during the Bosnian conflict.