The Hollywood couple made the donation via their charity, the Jolie-Pitt Foundation.
The money will go to the Education Partnership for Children of Conflict and will help 8,000 children who have lost parents, homes or the opportunity to go to school.
Jolie is known for her charity work and is a goodwill ambassador for the UN's Refugee Agency. She has visited Iraq twice in the past year.
The actress said in a statement: "These education support programmes for children of conflict are the best way to help them heal."
The couple hope other Hollywood celebrities will follow their lead and donate a portion of their earnings.
"We hope to encourage others to give to these great organisations," said Pitt.
During her last trip to Iraq in February, Jolie spoke of the urgent need for aid in the war-torn region.
"There are over two million displaced people and there never seems to be a real coherent plan to help them. There's lots of goodwill and lots of discussion but there seems to be a lot of talk at the moment and a lot of pieces that need to be put together," she said.
The 32-year-old Tomb Raider star is currently in France awaiting the birth of twins.
Their arrival will take the couple's brood to six - they are already parents to Maddox, six, Pax, four, Zahara, three, and Shiloh, two.
Earlier this month it was reported that Jolie had given birth, sparking a worldwide media frenzy, but the story turned out to be a hoax.
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