Despite earlier indicating that up to 40 suspected insurgents were killed in the air strike, a marine officer was later forced to admit that US forces had failed to find any bodies in the mosque.
"When we hit that building I thought we had killed all the bad guys, but when we went in they didn't find any bad guys in the building," Lieutenant Colonel Brennan Byrne told AFP.
Instead, he speculated the insurgents may have fled after a Cobra helicopter gunship fired a Hellfire missile at the mosque, and before an aircraft dropped a laser-guided precision bomb.
He also said it was possible other insurgents had dragged the bodies away in the 30-40 minutes before marines arrived to sweep the area.
Fallujah residents confirmed the Abdulaziz al-Samarai mosque was hit along with the building of the Islamic Scholars' Association.
The bomb hit the minaret of the mosque and ploughed a hole through the building, shattering windows and leaving the mosque badly damaged.
A Central Command spokesman said gunfire from within the mosque led US forces to bomb it, wounding five marines.
In Fallujah, an officer also told AFP a US Marine was shot dead by insurgents near the bombed mosque compound.
Earlier Wednesday, all the city mosque's called for a jihad, or holy war, against occupation forces, an AFP correspondent said.
A statement purportedly from insurgents claimed they had shot down three US helicopters, destroyed two jeeps and two armored vehicles.
They also said they were still in control of the city and had put US forces to flight, but Byrne said marines had reached the center of Fallujah.
Elsewhere, a US soldier was killed by rocket propelled grenade (RPG) fire early Wednesday as his convoy was relieving security forces guarding the Diala police station in Baghdad, the US military said.
First a warplane fired off guns, then a Cobra helicopter shot off a Hellfire missile at the mosque and finally an aircraft dropped a laser-guided precision bomb, Byrne said.
The roar of jets shook the city, caught in the midst of a brutal urban battle pitting the marines against the insurgents who have bled the coalition forces for months and ambushed and mutilated four US contractors last week.
Byrne said the marines carried out the raid as precisely as they could because there are people live nearby. Marines also came under RPG fire from guerrillas in a second mosque Wednesday.
The head of the Marines First Division, General James Mattis, defended the attack, warning if rebels used places of worship in their war against US forces, his troops would not hesitate to strike them at sacred sites.
"If they barricade themselves inside a mosque, we are not going to care about the mosque anymore than they do," Mattis said.
US forces have claimed the rebels use mosques to fire on them and hide weapons.
During fighting at the Fallujah mosque before it was bombed, police were seen supplying the insurgents with weapons and some police were even seen joining in the firefight, witnesses said.
An ambulance also drove up to the mosque, loaded with RPGs and fired rounds at the Americans, according to the marines.
Meanwhile, Byrne said the marines advancing from the south reached the center of Fallujah amid fierce fighting on the third day of "Operation Vigilant Resolve" to root out the insurgents who have plagued the US-led occuaption of Iraq.
"The marines are now at the center of the city," he told AFP.
It was not immediately clear if marines advancing from the north had also reached the center of Fallujah, which lies west of Baghdad.
One marine was shot in the arm in a separate attack by insurgents, an officer said on condition of anonymity.
The officer said a helicopter gunship shot and killed one insurgent who had fired a rocket-propelled grenade on marines Wednesday.
The body of an insurgent who was killed Tuesday was still lying on the ground of a street in southern Fallujah.