Roof was handed a Bible and worksheet as he sat in the prayer service for nearly 45 minutes before opening fire when the worshippers closed their eyes for the final prayer.
The conviction affirms the prosecution's argument that the 22-year-old hoped the killings would start a race war or bring back segregation.
In his confession to the FBI, the gunman said he carried out the killings after researching "black on white crime" on the internet.
He said he chose a church because that setting posed little danger to him.
Roof stared ahead of him as the verdict was read out.
In closing arguments, Assistant US Attorney Nathan Williams mocked Roof for calling himself brave in his hate-filled journal and during his confession, saying the real bravery came from the victims who tried to stop him as he fired 77 bullets at Emanuel African Methodist Episcopal church.
"Those people couldn't see the hatred in his heart any more than they could see the .45-caliber handgun and the eight magazines concealed around his waist," Mr Williams said.
The prosecutor said the good of all those faithful churchgoers prevailed over Roof's hatred.
"This defendant chose to take their lives. He chose to break their bodies. But he does not get to choose who they were," Williams added.
Defence lawyer David Bruck conceded Roof committed the killings, but he asked jurors to look into his head and see what caused him to become so full of hatred, calling him a suicidal loner who never grasped the gravity of what he did.
Jurors will reconvene early next month to hear more testimony and decide whether Roof gets the death penalty or life in prison.
