Jones and his associate Wayne Sapp had planned to demonstrate outside the Islamic Center of America in a suburb of the city of Dearborn, which is home to the largest concentration of Muslims in the US.
A local judge jailed the two after a court ruled that their planned action could lead to violence and they refused to pay a symbolic dollar each bail.
In court, Jones argued that the Koran "promotes terrorist activities around the world" and claimed that his right to protest against Islam was protected by
the US Constitution.
"The First Amendment does us no good if it confines us to saying what is popular," he said.
But Dearborn Police Chief Ronald Haddad testified that his department had received information about serious threats made against Jones from local residents, arguing that his protest could lead to violence if allowed.
The jury accepted Prosecutor Robert Moran’s argument that the protest had nothing to do with the First Amendment and that the community's security and peace were at stake.
After spending an hour in jail, the two changed their minds and posted the bond, local media reported.
The judge's ruling bans both Jones and Sapp from going to the mosque for three years. But Jones was quoted by The Detroit Free Press as saying the two "will come back next week" to try to organise a new protest.
Hundreds of local residents who rallied in front of Henry Ford Centennial Library late Friday denied they tried to silence free speech and pledged to remain peaceful.
Jones and Sapp made international headlines after their ceremonial "trial and execution" of the Koran by burning the Islamic holy book on 20 March at his Florida church.
It led to protests in Afghanistan, which resulted in seven UN staff being killed in the northern city of Mazar-i-Sharif and 17 others elsewhere.