The same jury last month found Roof, 22, guilty of 33 federal charges, including hate crimes resulting in death, for the shocking mass shooting at the landmark Emanuel African Methodist Episcopal Church in 2015.
Roof, pictured, who represented himself and did not argue against the death penalty, showed no emotion as the verdict was read.
Prosecutors said he planned the shooting for months, intending to incite racial violence by targeting the oldest African-American congregation in the US South.
"He decided the day, the hour and the moment that my sister was going to die, and now someone is going to do the same for him," Melvin Graham, brother of shooting victim Cynthia Hurd, 54, said outside the federal courthouse in the heart of historic Charleston's downtown district.
Roof will be formally sentenced on Wednesday. He also faces the death penalty if convicted of murder charges in a pending state trial. Roof did not present any evidence during the penalty phase that began last week or allow jurors to hear details about his mental health.
Roof was unrepentant during his short closing argument, telling jurors he still felt the massacre was something he had to do.
"Anyone who hates anything has good reason for it," he said. "I have a right to ask you to give me a life sentence, but I'm not sure what good that will do anyone."
On June 17, 2015, Roof sat for 40 minutes with parishioners gathered for a Bible study meeting before opening fire as they closed their eyes to pray.