Jones said Nadarkhani faces execution.
According to the report, the Pentagon urged Jones to reconsider, expressing concern that American soldiers in Afghanistan and elsewhere could be put at greater risk because of the act.
In March 2011, Jones' assistant, pastor Wayne Sapp, burned a copy of the Koran and broadcast the ceremony on the Internet.
The images incited violence in northern Afghanistan, in which at least 12 people were killed.
Later, a man wearing an Afghan border police uniform shot dead two US military personnel.
About 20 people attended Saturday's burning, the paper said. Several Gainesville police officers were stationed across the street from the church.
Moments after the ceremony, the Gainesville fire department issued the church a citation for violating the city's fire ordinances, the paper noted.