Celebrants said the accused gunman, 21-year-old Dylann Roof, had failed miserably in his quest to break their spirit of love and faith.
"There they were in the house of the Lord, studying your word, praying with one another," said visiting minister John Gillison from the pulpit.
"But the Devil also entered. And the Devil was trying to take charge," he said.
"Thanks be to God, hallelujah, that the Devil cannot take control of your people. And the Devil cannot take control of your church."
The crowd spilled into the street, where loudspeakers relayed songs and sermons from the two-hour service live to hundreds of worshipers braving brutal summer heat.
On the Arthur Ravenel Bridge, several thousand people later held hands in a "unity bridge" from Charleston to the affluent suburb of Mount Pleasant, observing nine minutes of silence - one for each of the victims.
The victims, aged 26 through 87, notably included Emanuel's chief pastor Clementa Pinckney, 41, also a respected South Carolina state senator who campaigned for tighter gun laws.
A website apparently created by Roof features a 2,500-word racist screed against African Americans, in which he appears in photos holding guns and the Confederate flag, and burning the Stars and Stripes.
Roof went on the run after the shooting and was caught a day later in neighbouring North Carolina. He is in solitary confinement charged with nine counts of murder.