Pastor Randy Flanagan said members of the congregation weren't star-struck — or didn't show it too much — when the Hollywood couple showed up on Christmas Eve with their daughter.
Violet's cousin Alex was also baptized.
Garner, a Charleston native, won a Golden Globe Award for her starring role as agent Sydney Bristow in the TV series "Alias," which ended its five-year run in May. Movie credits for the 34-year-old actress include "Elektra" and "13 Going on 30."
Affleck, also 34, is nominated for a Golden Globe Award for playing George Reeves, star of the 1950s TV show "Adventures of Superman," in "Hollywoodland." He won a screenwriting Oscar with Matt Damon in 1998 for "Good Will Hunting."
The couple were married in June 2005.
Garner's younger sister, Susannah, and her husband are also members of the church.