"It's artillery you hear ... (and) AC-130 aircraft are engaging known weapons caches in southeastern Fallujah," said marine spokesman Lieutenant Lyle Gilbert.
An AFP correspondent reported thunderous booms shaking the city's southern Shuhada district. Flames lit the sky, while US aircraft droned overhead, he added.
Gilbert said the attacks on the weapons warehouses were triggering secondary explosives.
Earlier, marines and insurgents clashed when rebels fired on marine positions with "small arms, RPGs (rocket-propelled grenades) and mortars near the city" at 5 pm (1400 GMT), the military said.
"Marines countered these attacks with substantial and proportionate ground fires and air-delivered precision strikes."
The city has seen almost daily strikes on suspected safe houses of Zarqawi, blamed for many of the car bombings and kidnappings in Iraq.
Separately, marine spokesman Lieutenant Robert Shuford said a tank was twice targeted by a traffic control point on the outskirts of the city.
"In the first attack, there were no casualties," he told AFP.
"The tank engaged with the enemy and took care of it," said Shuford.
There were no US casualties, but Shuford was unable to give any details on the assailants.
In other small-scale incidents, marines found a number of roadside bombs around the area, the spokesman said.
Determined to regain control of the no-go zone, more than 1,000 joint forces have encircled the city since Friday. Iraqi Prime Minister Iyad Allawi last week ordered Fallujah residents to surrender Zarqawi or face invasion.
Humanitarian agencies have raised concerns for the welfare of residents in the Sunni Muslim bastion amid near nightly US air raids.
Living conditions have deteriorated along with security in Fallujah, a city of 200,000 people, controlled by armed militants, that is often sealed off from the outside world. Residents who have fled the city warn of food shortages and power black-outs.
Islamic militants are said to have imposed a harsh form of Islamic law on the city, whipping people in public for acts like drinking alcohol.