Thursday's dawn raid was described as the latest in a series of "precision" attacks on Abu Musab al-Zarqawi and his alleged network.
A US military statement said "credible intelligence sources" reported that those killed had been planning attacks on innocent civilians and Iraqi security forces.
But the press release did not name those who were killed in the "precision" bombing.
The besieged city's main hospital denied the strikes were precise. Hospital spokesman Dr Ahmad Khalil said all three were civilians.
The owner of one of the destroyed homes said two of the victims were his brothers, who both worked in a grocery shop.
US troops have encircled Falluja and repeatedly launched air strikes and some limited ground incursions for months.
Iraq's appointed interim Prime Minister Iyad Allawi said on Tuesday his administration had still not ruled out a negotiated end to the stand-off between US troops and those opposed to their presence in Falluja.
Talks between the US-appointed government and delegates from the region collapsed in mid-October after Allawi ordered the city to surrender al-Zarqawi and other militia members.
Within hours of the bombing raid, one US soldier was killed and two more were wounded when a car bomb ripped through their vehicle patrol on a main road in southern Baghdad on Thursday morning.
Fallujans have had to endure
almost daily bombing raids
Lt Col James Hutton confirmed the toll from the 07:30 attack. Witnesses saw one US army vehicle burst into flames before the whole area was sealed off.
The dead soldier was from One Task Force Baghdad. A second Iraqi civilian may also have died in the blast, the military said.
"I heard the blast," said Amir Hasan, a security guard. "I
rushed up to the roof of the centre to look at what happened I saw one US military vehicle on fire and a lot of smoke coming from the area."
The blast occured under a flyover along the main road out of Baghdad to the southern cities of Hilla and Najaf.
Meanwhile, two Iraqi policemen and their driver were killed and four others injured in overnight attacks near the city of Baquba, a witness said on Thursday.
Ibrahim Muhammad said unknown assailants opened fire on the police officers as they entered the Abu Sayda station in the city's northeastern district.
Unknown attackers also opened fire on an Iraqi National Guard patrol a few kilometres away at the Ghalbiya checkpoint.
Iraq's fledgling police and guardsmen have been increasingly targeted in fighting that has shaken the country on a daily basis since last year's US-led invasion.