The money will fund food, blankets and clothes for communities who have been left destitute and isolated after heavy rains destroyed crops and homes.
News reports estimates that at least 42 people have been killed and as many as quarter of a million people have been displaced as a result of the floods.
The Rev Dr Chad Gandiya, USPG's Regional Desk Officer for Africa, said: "I witnessed terrible flooding in southern Angola and around Odibo in northern Namibia. It was heart-breaking to see. This grant will help the Anglican Church in both areas to reach out to people in extreme hardship."
Former USPG Mission Companion Nancy Robson, now retired and living in Odibo, Namibia, said: "The president has now declared a State of Emergency. Never has the country experienced the flooding like this before. Innumerable homes have been submerged, millet stores lost and most gardens have been 'drowned' as a result.
"Almost the whole of Ohangwena town is under water. A clinic that was housing cholera patients has had to move to tents in the Omafo area. Schools have had to close. Some children were coming to school with water chest high, carrying their clothes on their heads."
Ms Robson added that roads had been closed due to flooding, turning a 5k trip from Ohangwena to fetch supplies in Oshikango into a 55km round trip.
In Angola, Bishop Andre Soares said: "Families have been forced out of their homes, trying to rescue their possessions. They are now pleading for clothes, blankets, medicine and mattresses."Some have been put in temporary accommodation in schools, but the majority are in open camps, provided by the local government, without insufficient security, hygiene and shelter.
"The church is playing a very important roll in showing charity and love to the community."
USPG has sent £1,000 each to the Anglican Churches in both Angola and Namibia.
Support USPG as it helps Anglican Churches to provide emergency aid at times of natural disaster by clicking - HERE
