Denis Mukwege was awarded the prize for his work as a gynecologist treating victims of sexual violence in the Democratic Republic of Congo.
Nadia Murad fled Islamic State (ISIS) after being held as a sex slave in Iraq.
The Yazidi is a human rights activist.
The prize, worth nine million Swedish crowns ($1 million), will be presented in Oslo on December 10, the anniversary of the death of Swedish industrialist Alfred Nobel, who founded the awards in his 1895 will.
The Norwegian Nobel Committee said it had awarded them the prize for their efforts to end the use of sexual violence as a weapon of war.
In its announcement the committee said: “Both laureates have made a crucial contribution to focusing attention on, and combating, such war crimes.”
Mr Mukwege leads the Panzi Hospital in the eastern city of Bukavu.
Opened in 1999, the clinic receives thousands of women each year, many of them requiring surgery from sexual violence.
Ms Murad is an advocate for the Yazidi minority in Iraq and for refugee and women’s rights in general. She was enslaved and raped by Islamic State fighters in Mosul in 2014.