Jones burned copies of the Koran and an image depicting Muhammad on Saturday evening in front of his church Dove World Outreach Center in Gainesville, Florida, OCALA.com reports. Gainesville police were stationed near the church and patrolled the area.
The event, attended by around 20 people, was streamed live over the Internet.
Gainesville Fire Rescue issued the church a citation for violating the city's fire ordinances. Fire Chief Gene Prince was quoted as saying that Jones had approval for a burn but did not have the required authorisation to burn books, which can harm environment. The fine is $271, which includes court costs.
"The burning of a sacred text is wrong and unwarranted. The burning of the Koran is especially grievous to Muslims and does not reflect the biblical values nor the spirit of the Lord Jesus whom we serve," Dr Geoff Tunnicliffe, secretary general of the World Evangelical Alliance (WEA), said in a statement Saturday.
"We appeal to Islamic leaders worldwide to understand that this self-proclaimed antagonist does not represent Christians. Indeed he violates the call of Jesus to love people everywhere. Such violence does harm to us all."
Jones' public burning followed a personal meeting and intense conversation just one day earlier with representatives of the WEA, including Tunnicliffe.
The WEA said in a statement: "Tunnicliffe had personally challenged Jones to listen to fellow Christian leaders from North America – and if not them – at least hear concerns of a Christian pastor from an Islamic country. Rev Daniel Ho of Kuala Lumpur, Malaysia was at the meeting requesting that Jones divert from this course of action, along with Dr Joel Hunter, pastor of Northland Church in Orland and Dr Brian Stiller, Global Ambassador for the WEA. The group met with Jones for approximately 90 minutes."
Leith Anderson, president of the National Association of Evangelicals, said in a statement after the burning incident Saturday: "The handful of people taking this action represents no one but themselves. They periodically make threats that are offensive to Christians, Muslims and peace-loving people everywhere."
The Pentagon had also reportedly urged Jones to reconsider his plan, expressing concern that it could put US troops in Afghanistan and elsewhere at greater risk.
Although his previous protests attracted violent reactions in various parts of the world, Jones had told The Christian Post he would burn Korans and speak on "the last 1,400 years of Islamic persecution of Christians, believers, nonbelievers, homosexuals, and women".
Pastor Youcef Nadarkhani, who has been imprisoned in Iran for his Christian faith since October 2009, represents "all of the death and destruction caused by Islam, and the apathy and the lack of us really doing anything. Of course if our government would put pressure on Iran, we could do more, [as well as] with the help of the United Nations", he added.
"Christians don't burn Korans," said Mr Anderson. "Our Christian faith calls us to respect and love."
In July 2010, Jones threatened to burn 200 Qurans on the 10-year anniversary of the September 11, 2001 attacks on the World Trade Center in New York City. He deemed the controversial event "International Burn a Koran Day". Although he cancelled the event, his threat to burn the Muslim holy books sparked riots in the Middle East and Asia.
Another event in 2011 caused even more concern when Jones held the "trial of the Koran" in March inside his church. He burned the Islamic book, prompting massive riots in Northern Afghanistan city of Mazar-i-Shairf. Protesters attacked the United Nations Assistance Mission, reportedly killing 10 UN staff members.