This story has been updated.
Pinckney, 41, was leading a Bible group when a white gunman opened fire inside the historic African American church on Wednesday, killing nine.
In a statement last week, Biden decried "the senseless actions of a coward" and recalled that he last saw Pinckney at a 2014 prayer breakfast in Columbia.
"He was a good man, a man of faith, a man of service who carried forward Mother Emanuel’s legacy as a sacred place promoting freedom, equality, and justice for all," Biden said.
The president also noted that he and first lady Michelle Obama knew Pinckney.
The pastor's funeral is scheduled for 11 a.m. Friday at TD Arena on the College of Charleston campus.
Speaking on the South Carolina Senate floor just weeks before his death, Pinckney said that his faith required forgiveness, even of those who kill.
"The Lord teaches us to love all," he said, "and we pray that over time, justice will be done."