The same jury last month found Roof, 22, guilty of 33 federal charges, including hate crimes resulting in death, for the shootings at the historic Emanuel African Methodist Episcopal Church.
Jurors deliberated for less than three hours.
Roof showed no emotion as the verdict was read, Charleston’s Post and Courier newspaper reported.
“Justice is served in Charleston,” Malcolm Graham, shooting victim Cynthia Hurd’s younger brother, said in a post on Twitter following the verdict. “There’s no place in a civilized society for hatred, racism or discrimination.”
Roof, who represented himself for the penalty phase, was unrepentant during his closing argument earlier in the day.
He told jurors he still felt the massacre was something he had to do and did not ask that his life be spared.
A U.S. prosecutor argued that Roof deserved to die because the shooting was calculated and intended to incite racial violence.
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, Assistant U.S. Attorney Jay Richardson said.
Roof pulled the trigger 75 times as he methodically killed Hurd, 54; Clementa Pinckney, 41, the church’s pastor and a state senator; DePayne Middleton Doctor, 49; Sharonda Coleman Singleton, 45; Susie Jackson, 87; Ethel Lance, 70; Myra Thompson, 59; Daniel Simmons Sr., 74; and Tywanza Sanders, 26.
“Today’s sentencing decision means that this case will not be over for a very long time,” Roof’s lawyers, who represented him for the guilt phase, said in a statement.
“We are sorry that, despite our best efforts, the legal proceedings have shed so little light on the reasons for this tragedy,” said the lawyers, who objected to Roof’s self-representation.
Roof also still faces a trial on murder charges in state court, where prosecutors also are seeking the death penalty.