Sunday's event was presented as a trial of the book in which the Koran was found "guilty" and "executed."
The jury deliberated for about eight minutes. The book, which had been soaking for an hour in kerosene, was put in a metal tray in the center of the church, and Sapp started the fire with a barbecue lighter.
The book burned for around 10 minutes while some onlookers posed for photos.
Jones had drawn trenchant condemnation from many people, including US President Barack Obama, Secretary of State Hillary Clinton and Secretary of Defense Robert Gates, over his plan to burn the Muslim holy book in September.
He did not carry out his plan then and vowed he never would, saying he had made his point.
But this time, he said he had been "trying to give the Muslim world an opportunity to defend their book," but did not receive any answer.
He said he felt that he couldn't have a real trial without a real punishment.
The event was open to the public, but fewer than 30 people attended.
Life in the normally quiet city of Gainesville is centered around the University of Florida. And while there were public protests against Jones' 9/11 activities, this event was largely ignored.
Jadwiga Schatz, who came to show support for Jones, expressed concern that Islam was growing in Europe.
"These people, for me, are like monsters," she said. "I hate these people."
Jones said he considered this event a success.
"This is a once-in-a-lifetime experience," he said.
----------------------------------------------------------------------------------