The wife and youngest daughter of a pastor who was murdered along with eight parishioners were inside the church during the shooting rampage, it has emerged.
The Rev Clementa Pinckney's wife Jennifer and her daughter were in the pastor's study when the shooting happened on Wednesday night, the Rev Norvel Goff, interim pastor of the Emanuel African Methodist Episcopal Church in Charleston, South Carolina, said. They locked the door, hid under the desk and called 911.
"It was awful and horrible and unthinkable and evil," Mr Goff said.
Mr Goff, who left the church 20 minutes before the Bible study began that night, said he had been conducting a quarterly business conference with about 50 church leaders, including Mr Pinkney and his wife.
Dylann Roof, 21, is charged with nine counts of murder over the death of the parishioners.
Yesterday, four days after it welcomed a young stranger who sat for prayer then opened fire, the church held its first worship service with themes of love and healing, plus a note of defiance.
"Some folks might need some more time in order to walk in," said Mr Goff. "But for those of us who are here this morning ... because the doors of Mother Emanuel are open on this Sunday, it sends a message to every demon in hell and on earth."
The church's air conditioning did little to fight the heat of extra bodies in the sanctuary. Many stood, some holding small children, to shout their praises.
Police officers stood watch over the worshippers at one of the oldest black congregations in the US South. Some congregation members stood to applaud when Mr Goff thanked law enforcement for their response to the shooting, which once again called up deep questions about race, and guns, in America.
A black sheet was draped over Pinckney's usual chair, which sat empty. At least one parishioner kneeled down in front of it and prayed.
Mr Goff acknowledged it was Father's Day and said: "The only way evil can triumph is for good folks to sit down and do nothing."
Later, thousands of people gathered on the Arthur Ravenel Bridge to join hands in solidarity. The bridge's namesake is a former state politician and a vocal supporter of the Confederate flag carried by pro-slavery, secessionist forces in the American Civil War.
The shootings have renewed calls for the flag to be removed from the South Carolina Statehouse grounds. Photographs of Roof, along with a purported hate-filled manifesto online, showed him holding Confederate flags.
Less than two miles from the church, someone vandalised a Confederate monument, spray-painting "Black Lives Matter" on the statue. The slogan emerged during protests over police killings of unarmed black men in several US cities over the past year.
City workers used a tarpaulin to cover up the graffiti.
Around the country, pastors asked people to pray for Charleston.
In a sign of resilience, the church's Wednesday night Bible study is expected to continue as normal next week, said Emanuel member Harold Washington, 75.
"We didn't change a thing," he said.
Churchgoers across America prayed for the nine shooting victims, with pastors of all denominations f rom Little Rock, Arkansas, to Atlanta, Chicago and Portland, Maine, urging their Sunday service flocks to stand in unity with the families and to resist the hatred that appeared to be behind the killing.
In Chicago, religious leaders held an inter-faith, inter-racial prayer service at New Mount Pilgrim Missionary Baptist Church.
"We can't let hate win," church pastor the Rev Marshall Hatch said.