The smoke on Friday shrouded the southeastern industrial zone, which houses mainly metal and mechanical workshops, as residents charged that US forces had lobbed artillery into the area, although warplanes were also sighted.
Within minutes, the artillery fire was followed by an air strike on the Shuhada district in southern Falluja.
A marine spokesman confirmed artillery had been fired on the outskirts of the city after troops spotted fighters in a vehicle with a mounted weapons system. The vehicle managed to flee, he added.
The US military has intensified its strikes on Falluja this month, targeting suspected hideouts of alleged top al-Qaida operative Abu Mussab al-Zarqawi.
The town, 50km west of Baghdad, has been a no-go zone for US troops since a deadly offensive there in April ended in a stand-off.
Earlier, Abd al-Salam al-Kubaisy, member of the Iraqi Muslim Scholars council, slammed the United Nations for turning a blind eye to the "US aggression in Iraq, especially in the cities of Falluja, Samarra and Najaf".
Speaking at a large rally near Abu Ghraib prison, al-Kubaisy called on UN Secretary General Kofi Annan to speak out against the US actions in Iraq.
He also urged the Iraqi National Guards and police "not to be used as a cover for the occupation troops".
Meanwhile in Baghdad, five mortars fell near the Italian embassy in al-Wizairyia neighbourhood, wounding two women and damaging four houses in the area.
Black smoke was seen rising in the area, while US troops and members of Iraqi national guards rushed to the site and started a search campaign for the attackers in nearby neighbourhoods.
The Italian embassy in Baghdad
was previously targeted in July
The Italian embassy came under a similar mortar strike in July in which six Iraqi civilians were injured.
Friday's attack came as the lives of two Italian female aid workers held hostage in Iraq hung in the balance.
In a separate development, an explosive device blew up under a US military convoy on the highway west of Baghdad, between Falluja and Ramadi, sources told Aljazeera.
One vehicle was destroyed and several US soldiers were injured in the attack. US helicopters were seen landing near the blast site to carry away wounded soldiers.
Shia mosque hit
Overnight, a Shia mosque in Baghdad was struck by mortar shells, the US military said on Friday, without reporting casualties.
The military identified the damaged site as Kadhimiyah mosque. "One round left a three-foot (one-metre) hole in the dome of the Kadhimiyah mosque on the city's south side," the US military said in a statement.
"Besides damage to the dome, one round landed in the facility's courtyard and a third landed in the street just outside the building," according to the statement.