Rudolph was 12 at the time, and her family left the church after the bombing. She said it was important to return in memory of her sister, who was 14, and the three other girls who died: Carole Robertson and Cynthia Wesley, both 14, and Denise McNair, 11.
"God spared me to live and tell just what happened on that day," said Rudolph, who testified against the Klansmen convicted years later in the bombing.
Congregation members and visitors sang the old hymn "Love Lifted Me" and joined hands in prayer. The somber Sunday school lesson was followed by a raucous, packed worship service with gospel music and believers waving their hands.
During the sermon, the Rev. Julius Scruggs of Huntsville, president of the National Baptist Convention USA, said, "God said you may murder four little girls, but you won't murder the dream of justice and liberty for all."
Later Sunday, Attorney General Eric Holder and others attended a commemoration. Former Secretary of State Condoleezza Rice, a Birmingham native who went to school with McNair, was among the speakers.
The dynamite bomb went off outside the church Sept. 15, 1963. Of the Klansmen convicted years later, one remains imprisoned. Two others died in prison.
Two young men, both black, were shot to death in Birmingham in the chaos that followed the bombing.
Birmingham was strictly segregated at the time of the bombing, which occurred as city schools were being racially integrated for the first time. The all-black 16th Street Baptist was a gathering spot for civil rights demonstrations for months before the blast.
President Barack Obama issued a statement noting that earlier this year the four girls were posthumously awarded the Congressional Gold Medal, one of the country's highest civilian honors.