olice are treating the killings at the church in Charleston on Wednesday night as a hate crime.
Earlier, Dylann Roof, 21, appeared in court 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.
Speaking in San Francisco, Mr Obama said: “The apparent motivations of the shooter remind us that racism remains a blight that we have to combat together.
“We have made great progress, but we have to be vigilant because it still lingers.
“And when it’s poisoning the minds of young people, it betrays our ideals and tears our democracy apart.”
But the president praised the families of the victims for the forgiveness they had shown.
He said it was “an expression of faith that is unimaginable but that reflects the goodness of the American people”.
Mr Obama also called for a new debate on gun control, and pushed Congress to follow public opinion.
“It’s not enough for us to express sympathy; we have to take action,” he said.
A previous proposed bill banning assault weapons failed to win backing in the Senate.
At a Charleston sports arena, thousands gathered on Friday evening to remember the victims with prayers. They joined hands to sing We Shall Overcome.
Ahead of the vigil, Mayor Joseph Riley said: “A hateful person came to this community with some crazy idea he’d be able to divide, but all he did was unite us and make us love each other even more.”
A steady stream of people also brought flowers to place at a memorial in front of the church.