It was only the sixth loss - and third in regulation - for the United States in 28 matches since the tournament began as the U-19 championship in 2002. It also was the most lopsided defeat for the Americans, eclipsing a 3-1 loss to Germany in 2004 and a 2-0 loss to China in 2008.
The result finished the United States in second place in Group D with four points, five behind Germany and ahead of third-place China on goal difference. China defeated Ghana 1-0 in a match played simultaneously in Saitama.
It pits the Americans against Group C winner North Korea in the knockout round on Friday. The United States beat North Korea for the 2008 title in Chile.
Lena Lotzen scored in the 35th and 53rd minutes for Germany, and Melanie Leupolz added another in the 55th.
Lotzen headed over an onrushing U.S. keeper Bryane Heaberline to put Germany ahead, knocked in a rebound after Heaberline failed to Lina Magull's shot, and Leupolz scored from 15 meters after the United States was unable to clear the ball from the area.