The discovery, one of several finds by a team from Sweden's Lund University, was made near Aswan, 850 kilometres (528 miles) from the Egyptian capital.
The wall relief is one of the "few available sculptures combining the two deities -- God Amen-Re and God Thot," Ali al-Asfar, head of Upper Egypt's antiquities, told AFP.
Thot, the ancient god of wisdom, is depicted with the body of a man and face of an ibis sacred bird.
The wall relief was found in a quarry north of Aswan used to supply stone to build the famed Karnak and Luxor temples in the city of Luxor.