The incident happened shortly before 2 a.m. at the restaurant on Jonesboro Road just off Interstate 85 in Union City.
Union City Police Det. Gloria Hodgson said the suspect, who was armed with a pistol, entered the Waffle House and demanded money.
A customer sitting inside the restaurant shot the suspect. He was taken to Grady Memorial Hospital; his condition was not immediately known.
No names were released. Hodgson said no one else was injured.