Barack Obama delivered a eulogy for his friend before singing the famous hymn, written by John Newton.
Nine black people were killed in total in the Charleston attack. A white man, 21-year-old Dylann Roof, has been remanded in custody in connection with the murders.
Some families of the deceased used their victim statements to publicly call Mr Roof to accept Jesus Christ as his Lord and Saviour, forgive him for the attack, and ask for God to have mercy on his soul.
Mr Obama said in his eulogy: "Blinded by hatred, the alleged killer could not see the grace surrounding Revd Pinckney and that Bible study group. The light of love that's shown as they opened the church doors and invited a stranger to join in their prayer circle.
"The alleged killer could have never anticipated the way the families of the fallen would respond when they saw him in court in the midst of unspeakable grief with words of forgiveness.
"As a nation, out of this terrible tragedy, God has visited grace upon us for he has allowed us to see where we've been blind. He's given us the chance, where we've been lost, to find our best selves."
Watch a video of Barack Obama's eulogy here.
