The donation to the Naankuse Lodge and Wildlife Sanctuary was made through the Jolie-Pitt Foundation in the name of their daughter Shiloh, who was born in Namibia.
In a statement released late Sunday, Angelina said, "We want her to be very involved and grow up with the understanding of her country of birth."
Angelina said Rudie and Marlice van Vuuren, the owners of the sanctuary, are old friends. "We continue to be impressed by their hard work and dedication to the people and conservation of the land and wildlife of Namibia," she said.
The Jolie-Pitt family spent Christmas together at the exclusive lodge, where staff say the children helped to feed and care for orphaned baby baboons and foxes and saw a leopard released back into the wild.
The van Vuurens said in the statement that they were "overjoyed" that Angelina and Brad chose Naankuse as the foundation's partner in Namibia.
Dara Barrett, head of finance at the Naankuse sanctuary, told The Associated Press that the money would be used primarily to benefit the community of San bushmen on the farm and surrounding areas.
"Some of the donated funds will be used in the running of a clinic which provides free medical care to the community of bushmen, including the treatment of malnutrition, tuberculosis and HIV," she said.
The remainder of the funds will be used for large animal conservation projects and other San community projects which have yet to be identified, Barrett said.