"We want to contribute to Namibia and the people who have been so gracious to us at this time," Pitt, 42, and Jolie, 30, are quoted as saying in the statement.
Namibia's Deputy Environment and Tourism Minister, Leon Jooste, says the money will be used to improve maternity wards at hospitals in Walvis Bay and Swakopmund and will contribute significantly to the health of Namibian babies.
Although Shiloh was born at a private facility, most Namibians rely on state hospitals like the ones that will benefit from Pitt and Jolie's gift, the Associated Press reports.
The new parents also pledged $15,000 for a school and a community center that they had visited in Swakopmund.
Earlier, Jooste had announced, "Shiloh Nouvel Jolie-Pitt will, according to Namibian law, be allowed to obtain Namibian citizenship, if the parents should choose to do so." He added that discussion of the child's passport will be taken up with her parents "at a later stage."
"Angie and baby are fantastic," a source close to the couple told PEOPLE on Sunday. "Brad was at her side during the birth."
While Namibian officials declined to give details on the birth, a doctor at the hospital said there were no complications and the mother and daughter were doing well.
"She is a healthy baby," the doctor told the AP, speaking on condition of anonymity because he was not authorized to release information.
Back in the U.S., the manager for Jolie's estranged father, Oscar-winning actor Jon Voight, 67, told New York's Daily News that Voight is "really excited for them both. He can't wait to hold the baby in his arms and be grandpa."
Pitt and Jolie, along with kids Maddox, 4, and Zahara, 1, have been staying at a luxury resort in Namibia since April, where their personal security team and Namibian police have shielded them from paparazzi.