Dylann Roof, 21, appeared in court in Charleston to face nine murder charges.
He showed no emotion as relatives of the victims addressed him directly. "I forgive you" said one victim's daughter, fighting back tears.
Police are treating the killings at the African-American church on Wednesday night as a hate crime.
And the Justice Department says it is investigating whether it might have been an act of domestic terrorism.
It said in a statement, the shooting was "designed to strike fear and terror into this community", and the department was considering all possibilities.
At a Charleston sports arena, thousands gathered on Friday evening to remember the victims with prayers and songs.
Also on Friday, the Roof family released a statement through their lawyer.
"Words cannot express our shock, grief and disbelief as to what happened that night. We are devastated and saddened by what occurred," the family wrote. "We have all been touched by the moving words from the victims' families offering God's forgiveness and love in the face of such horrible suffering."
In court in Charleston on Friday afternoon, Mr Roof spoke to confirm his name, age and address and said he was unemployed.
Then relatives were invited by the judge to come forward and speak.
A woman who identified herself as the daughter of Ethel Lance said: "You took something very precious from me. I will never talk to her ever again.
"I will never be able to hold her again, but I forgive you. And [may God] have mercy on your soul."
Anthony Thompson, a relative of Myra Thompson, told Mr Roof to repent and to turn to Jesus Christ.
"I forgive you and my family forgives you," he said.
Also speaking in court was Felecia Sanders, who survived the attack on Wednesday night by playing dead. Her son, Tywanza, was fatally wounded.
"We welcomed you Wednesday night in our Bible study with open arms. You have killed some of the most beautifulest people that I know. Every fibre in my body hurts ... and I'll never be the same," she said to Mr Roof, who appeared via a video feed.
The victims of the Charleston shooting
Meanwhile, one of Mr Roof's friends, Christon Scriven, told the BBC's Rajini Vaidyanathan that Mr Roof had considered a university as a potential target.
Mr Scriven said Mr Roof "wanted to shoot that school up, UCA University of Charleston. It's 3 miles up the street from that church".
But Mr Scriven, who is black, did not think Mr Roof would actually follow through.
"So how do you take it serious?" he said. "How many friends do you have in your lifetime that's killed somebody?"
Court documents have revealed new details about the shooting.
Mr Roof entered the church just after 20:00 local time (01:00 BST) on Wednesday night and remained with the worshippers for nearly an hour before launching his attack.
All of the victims were hit multiple times, the documents said.
Before leaving, Mr Roof stood over one person who was not shot and "uttered a racially inflammatory statement". That person has not been named, and has only been described as a "witness" in the court documents.
The judge set Mr Roof's bond at $1m (Â£630,000) for the weapons possession charge but could not place a bond on the murder charges due to a legal technicality and Mr Roof will remain in jail.
"Racist shooting stirs up America's worst ghosts," writes Spain's El Pais.
The US events are "so shocking that they are unspeakable," writes Italy's La Stampa.
"Pain, fear and anger have engulfed America after the shooting, exacerbating the racial demons of a deeply fractured society," says Frederic Autran, the New York correspondent for France's Liberation.
Writing in Russia's popular Moskovskiy Komsomolets daily, Melor Sturua accuses Mr Obama of ducking the real issue by opting to describe the killings as "senseless" rather than "racist".
In Iran, the conservative Fars News Agency says that "racism is a dark phenomenon which has its roots in the heart of the American society".
The official Xinhua agency in China said the violence "mirrors the US government's inaction on rampant gun violence as well as the growing racial hatred in the country".
Sources: BBC Monitoring, AP
Relatives of some of the nine churchgoers shot dead in South Carolina have addressed the suspected gunman in court and said they forgive him.