The suspect, Dylann Roof, 21, was detained while driving in Shelby, North Carolina, about 200 miles away.
After a court appearance on Thursday, Mr Roof waived his right to extradition and was flown back to South Carolina.
Six women and three men, including the pastor, died in the attack. A hate crimes investigation has been launched.
Several churches in Charleston were full to overflowing on Thursday evening as prayer services were held. Some services were held outdoors.
Outside the Emanuel AME Church, where the attack took place, hundreds gathered in soaring heat to pay tribute.
“We really have to fight together to go on and to live a civilised life where race doesn’t matter,” said one woman, Martha Watson.
At a vigil for victim Sharonda Singleton, her teenage children told the BBC they had forgiven the killer and wanted to focus on moving on in a positive way.
Services were held in several other cities, including Miami, Detroit and Philadelphia.
In New York, services and protests took place, with placards including such messages as “Black Lives Matter” and “Stop killing black people”.
Richard Price, executive assistant at the Harlem Church of Christ, said: “That someone would come and infiltrate that sacred space, one of the only spaces we ever really have, and to violate that space, and then to shoot the place up…
“This is a deep, deep-seated hurt that may never ever heal.”
A prayer vigil was also held outside the US Capitol. Senate chaplain Barry Black said: “Our hearts ache because, in the future, people will feel fear in the house of God when they should feel peace and serenity.”
US President Barack Obama said he and his wife had known several members of the Emanuel AME Church, including pastor, Clementa Pinckney.
Mr Obama called the church a “sacred place” in the history of Charleston and spoke of his confidence that the congregation and the community would “rise again”.
Richard Price, executive assistant at the Harlem Church of Christ, said: “That someone would come and infiltrate that sacred space, one of the only spaces we ever really have, and to violate that space, and then to shoot the place up…
“This is a deep, deep-seated hurt that may never ever heal.”
A prayer vigil was also held outside the US Capitol. Senate chaplain Barry Black said: “Our hearts ache because, in the future, people will feel fear in the house of God when they should feel peace and serenity.”
US President Barack Obama said he and his wife had known several members of the Emanuel AME Church, including pastor, Clementa Pinckney.
Mr Obama called the church a “sacred place” in the history of Charleston and spoke of his confidence that the congregation and the community would “rise again”.
The police chief in Shelby said Dylann Roof was arrested after a tip-off from a local florist, Debbie Dills.
“At first I thought, nah, it couldn’t be,” Mrs Dills said. “I didn’t want to overreact.”
Mrs Dills trailed the suspect’s Hyundai car while talking on the phone to police, who then pulled the car over near a supermarket.
Dalton Tyler, who said he was a friend of Mr Roof, told ABC News the suspect had spoken in support of racial segregation and had “said he wanted to start a civil war”.
Mr Roof had attended a Bible study group for nearly an hour at the church before becoming aggressive and violent, Charleston’s county coroner said.
Eight people died at the scene and one person died later in hospital. There were three survivors.
Along with Rev Pinckney, a 41-year-old father of two, the other victims have been named as Cynthia Hurd, 54; Tywanza Sanders, 26; Ms Singleton, 45; Myra Thompson, 59; Ethel Lance, 70; Susie Jackson, 87; the Rev Daniel Simmons Sr, 74; and DePayne Doctor.
Cynthia Taylor, a niece of Ms Jackson, said she had spoken to a survivor, Felecia Sanders, who said she had played dead as she lay on top of her granddaughter to protect her.
Police and officials were quick to call the attack a hate crime.
The Emanuel church is the oldest African Methodist Episcopal (AME) church in the US south. Civil rights leader Martin Luther King gave a speech there in April 1962.
Tensions have been heightened since the shooting two months ago of Walter Scott, an unarmed black man by a white police officer in North Charleston, which prompted angry protests.
The officer has since been charged with murder.
Rev Pinckney – who was also a Democratic state senator in South Carolina – had recently sponsored a bill to make body cameras mandatory for all the state’s police officers.
Source: 3news.com/Ghana
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