The 10 women and two men recommended the death penalty for all 18 counts that carried that as a possible sentence.
Roof will become the first federal hate crime defendant to be sentenced to death, a Justice Department spokesman said.
Judge Richard Gergel will formally sentence Roof on Wednesday at 9:30 a.m. ET. Roof, who represented himself during the penalty phase, told Gergel he wanted to file a motion for new lawyers. Gergel said Roof can argue that on Wednesday but he is not inclined to let that happen.
A group of defense attorneys and others who worked on Roof's behalf issued a statement, saying the death penalty decision means the case will not be over for a "very long time."
"We are sorry that, despite our best efforts, the legal proceedings have shed so little light on the reasons for this tragedy," the statement said.
The jurors did not look at Roof when they came in with the verdict. Several looked in the direction of the victims' families.
It was very quiet in the courtroom. There was no sound coming from the many family members.
Roof, who was facing away from the media, did not appear to show any reaction to the verdict.
Some of the people in the gallery were dabbing their eyes. Several relatives of those killed gently put their arms around each other.
"Today we had justice for my sister (Cynthia Hurd)," Melvin Graham told reporters. "This is a very hollow victory, because my sister is still gone. I wish that this verdict could have brought her back. But what it can do is just send a message to those who feel the way he feels that this community will not tolerate it."
Graham said he just wants mass killings to stop.
"Every time I hear about a shooting I want to cry," he said. "We have to stand together."
Roof's family said they will always love him.
"We will struggle as long as we live to understand why he committed this horrible attack, which caused so much pain to so many good people," they added. "We wish to express the grief we feel for the victims of his crimes, and our sympathy to the many families he has hurt."
The judge, who is bound by the jury's decision, complimented the jurors and said they did a magnificent job.
Prosecutors called the decision a result of hard work and said it was a "fair and just process."
US Attorney Beth Drake said Roof failed at his attempt to split people by race.
"Contrary to Roof's desire to sow the seeds of hate, his acts did not tear this community apart," she said. "Instead of agitating racial tensions as he had hoped, Roof's deadly attack inside Mother Emanuel became an attack on all of us, and the community stood in solidarity."
Roof: I had no choice
Before the jury deliberated his fate for three hours, Roof told the jury he still feels he had no choice but to kill nine people at the Emanuel African Methodist Episcopal Church in June 2015.
"In my confession to the FBI I told them that I had to do it, and obviously that's not really true. ... I didn't have to do anything," Roof said as he made his own five-minute closing argument in the penalty phase of his federal trial. "But what I meant when I said that was, I felt like I had to do it, and I still do feel like I had to do it."
But he also had suggested he'd like to be spared.
"From what I've been told, I have a right to ask you to give me a life sentence, but I'm not sure what good that will do anyway," Roof said. "But what I will say is only one of you has to disagree with the other jurors."
His statement followed a prosecutor's impassioned, two-hour argument in a Charleston courtroom urging jurors to give Roof the death penalty instead of their other option, life in prison without possibility of parole.
Jurors convicted Roof, an avowed white supremacist, last month of federal murder and hate crimes charges.
The prosecution and defense rested in the penalty phase on Monday, bringing to a close days of heartbreaking testimony from family and friends of victims who were killed.
Prosecutors argued that he's a calculating killer who deserves the death penalty because of his motive, his lack of remorse and the shooting's impact on the victims' families.
Prosecutor reminds jurors of gruesome details
In his closing argument Tuesday morning, Assistant US Attorney Jay Richardson described the lives of all nine victims, cited Roof's "racist hatred" and reminded the jurors of the testimony and evidence that convicted him:
• Roof was at the church three previous times to scout his target.
• He sat with the group for 40 minutes before shooting.
• He pulled the trigger "more than 75 times ... reloading seven times" as he stood over his victims, shooting them repeatedly.
• He "showed not one ounce of remorse."
• Richardson referred to what Roof had told investigators in a recorded interview: That "somebody had to do it," in part because "black people are killing white people every day."
"Those are the words of an extraordinary racist who believed it was justified," Richardson said.
Roof's jailhouse journal
Earlier in the penalty phase, prosecutors presented evidence that included chilling writings from a jailhouse journal Roof wrote after the attack.
"I would like to make it crystal clear. I do not regret what I did," Roof wrote in the journal. "I am not sorry. I have not shed a tear for the innocent people I killed."
Friends and relatives of victims slain in the shooting gave emotional testimony in court before Tuesday, some of them sobbing on the stand.
As they made their case, prosecutors played haunting recordings of the victims preaching, praying and singing.
Facing the death penalty
Roof is also set to be tried on state murder charges, and prosecutors have said they'll also seek the death penalty in that case.
Serial killer Gary Lee Sampson
was the last person to get a federal death sentence. He's one of 63 federal prisoners, including Boston Marathon bomber Dzhokhar Tsarnaev
, awaiting execution, according to the Death Penalty Information Center
, a Washington-based nonprofit.
Only three federal inmates have been executed
in the United States since the federal death penalty was reinstated in 1988 after a 16-year moratorium:
• Oklahoma City bomber Timothy McVeigh on June 11, 2001, six years after he killed 168 people.
• Juan Raul Garza on June 19, 2001, eight years after he was convicted of running a marijuana drug ring and killing three people.
• Louis Jones on March 18, 2003, eight years after he kidnapped and murdered 19-year-old Army Pvt. Tracie McBride.