Centro Cristiano de Columbia Church Pastor Henry Alfaro said people were kneeling in prayer in the dimly-lit Forest Acres church around 6:15 a.m. when a man with a gun entered, fired in the air and shot a church member before running off.
His gun appeared to stop working after he shot the parishioner, Alfaro told WLTX-TV in Columbia.
It wasn't immediately clear how many people were inside the church at the time.
The news outlet identified the wounded man as 23-year-old Esvin Perez. He underwent surgery and remained in a hospital.
Forest Acres police said the suspect sped off in a car.
No arrests have been made.