Aljazeera's correspondent in Baghdad reported that one man had died after an exchange of fire with US forces after they broke into a house in the town. One US soldier was also killed in the firefight.
Perpetual friction between
US troops and civilians
The other fatality was a gunshop owner mistaken for an assailant and shot as he repaired his Kalashnikov outside his store in the town's marketplace, witnesses said.
Today's deaths follow the killing of another Iraqi yesterday after US forces came under fire near a mosque on the town's outskirts. Another attacker escaped, said US Central Command.
Fallujah has been a hotbed of resistance since US forces occupied Iraq in mid-April after ousting Saddam Hussein.
Mounting US casualties forced Washington on Thursday to send in 1000 troops in a bid to snuff out resistance in the central Iraq town which is home to the Al-Dulaimi tribe, loyal to the former Iraqi president.
But the house-to-house raids have provoked further resentment among townspeople with accusations of heavy-handedness and disrespect for Islamic moral codes, especially in relation to the troops' dealings with women.
On Friday US soldiers escaped injury when a rocket-propelled grenade was fired at an armoured vehicle. A day earlier, one US soldier was killed and five wounded in an attack in the town.