Yuki Uema, an 18-year-old high school student, died in the hospital of injuries sustained in the October 7 accident, they said.
She never regained consciousness after the initial impact, hospital officials said.
CBS News Correspondent Barry Petersen reports that the incident has intensified Japanese protests of the American military presence on Okinawa and sent U.S. officials scrambling to contain the damage.
Japanese investigators said Uema was riding a motorcycle around 4.30 a.m. in a village in Okinawa when she was struck by a car driven by 23-year-old Randall Eskridge.
"This is a tragic, needless loss," said the commander of Japan's U.S. Marine Corps bases, Lt. Gen. Frank Libutti. "We know there is little we can say to ease the Uema family's pain and grief but we are very sorry."
The incident added further damage to already frayed relations between the U.S. military and Okinawa residents, many of whom want U.S. forces withdrawn from the southernmost Japanese prefecture.
In a rare criticism Thursday, Japan's Chief Cabinet Secretary Hiromu Nonaka expressed anger over Uema's death at a news conference, and said the U.S. should improve the standards of conduct of its troops in Japan.
"We would like to express our strong sense of regret to the United States government and ask them to take the strongest possible steps to prevent the recurrence of such an incident," Nonaka said.
The U.S. military on Tuesday handed Eskridge over to Japanese prosecutors, who have indicted him on charges of drunken driving, leaving the scene of an accident and professional negligence to cause injury.
Eskridge, a native of La Porte, Indiana, is a flight equipment technician at Futenma Marine Corps air station near the Okinawan capital, Naha.
The incident has prompted a flurry of official apologies from the U.S. government, including one from U.S. Ambassador to Japan Thomas Foley.
A Marine Corps spokesman said Marines on Okinawa this week are spending half a day in briefings on alcohol use and moral values. The sessions include a period of reflection on Uema's family, he said. The girl's funeral is scheduled for Friday.
The presence of nearly 27,000 U.S. servicemen on the island is an irritant that spilled over into outrage three years ago when three U.S. servicemen were accused of raping an Okinawa girl. They were convicted of the 1995 crime.
About 20 percent of Okinawa is occupied by U.S. bases, and although it has less than one percent of Japan's land mass, the island is home to 75 percent of U.S. forces in Japan.
The latest incident comes ahead of hotly contested Okinawa gubernatorial elections set for Nov. 15. The election is seen as a referendum on the U.S. military presence.