Jones, 61, the leader of a 15-member, non-denominational church in Gainesville, Fla., was jailed, charged with unlawfully transporting fuel, a felony, and openly carrying a firearm, a misdemeanor, Polk County Sheriff Grady Judd said Wednesday night.
Jones was riding in a pickup truck driven by Marvin Wayne Sapp, 44, an associate pastor at Jones' Dove World Outreach Center, Judd said.
The truck was towing a smoker-like grill and trailer filled with Korans, many soaked with kerosene.
Jones and Sapp also had extra bottles of kerosene inside the truck bed.
Sapp was charged with several civil traffic violations, including towing a trailer with no lights, safety chain or license plate, Judd said.
Both men spent the night in jail.
Sheriff's deputies had expected Jones ever since he announced on his church website he would burn 2,998 copies of the Muslim scripture -- one for each victim of the Sept. 11, 2001, attacks -- at 5 p.m. Wednesday in a park just north of Mulberry, Judd said.
Wednesday was the 12th anniversary of the terrorist attacks. Mulberry is about 30 miles east of Tampa.
Deputies saw Jones at a McDonald's restaurant in Mulberry and watched as he doused the books with kerosene before driving to the park, Judd told reporters.
They arrested him at 4:58 p.m., he said.
"He was told that if he was going to come to Polk County and violate the law, he would be going to jail," the sheriff said.
Dousing the Korans violated the law, if for no other reason than it created a public safety hazard, Judd said.
"He was potentially driving a bomb around if he had gotten into a crash," he said in remarks quoted by The Tampa Tribune.
Deputies seized Sapp's 1998 Chevrolet C/K pickup truck, along with the smoker and Korans, Judd said. All will be held in evidence until the case is resolved.
Judd said he was unsure what would happen to the Korans, the central religious text of Islam, which Muslims believe to be a revelation from God.
If they were destroyed by the kerosene, deputies will consult with local imams to see how to properly dispose of them, he said.
A couple-dozen people had gathered at the park to support Jones, the Tribune said.
"I think it was a setup," Lakeland resident Bill Berry told the newspaper.
"That's bull. Whether you agree with the man or not, he has the right to protest," Berry said.
Jones first gained national and international attention in 2010 for his plan to burn Korans on the ninth anniversary of the Sept. 11 attacks.
The Council on American-Islamic Relations says at least 800 Muslims of many nationalities were killed in the terrorist attacks.