The money comes from the couple's Jolie-Pitt Foundation and is going to the Community Foundation of the Ozarks. The foundation announced the gift Friday in a news release.
Pitt is from Missouri and said he spent much of his childhood in Joplin.
On May 22, a tornado ripped through Joplin, leaving 151 people dead and destroying more than 8,000 homes and 400 businesses.
The Associated Press contributed to this report.