Iraqi insurgents used the house in the city of Husayba to stage attacks against US and Iraqi forces while holding a family hostage, the US Marine Corps said in a statement.
"Subsequently, the house was destroyed by coalition aircraft," said the statement by the 2nd Marine Division headquartered in Ramadi.
"The soldiers and Marines had no knowledge of the civilians being held hostage in the home at the time of the attack," it said.
It was the believed to be the first official acknowledgement of civilian casualties in so-called "Operation Steel Curtain," which the US military said succeeded in wresting control of the city from insurgents.
The marines discovered the civilian casualties during clearing operations when they were approached for help by an elderly local man, the command said.
"Based on information from the man, Iraqi soldiers and marines rescued two civilians, an adult male and a young girl, from a building coalition air strikes destroyed on Nov 7," it said.
The survivors were taken to the nearby town of al-Qaim for medical treatment, the marines said.
"Five bodies have been found by the Iraqi soldiers and Marines excavating the site," the statement said.
The Iraqi who led the marines to the casualties said insurgents broke into the house during the fighting, killed two people and then forced the rest of the family into a locked room in the lower level of the house, it said.