The court also ordered the immediate release of Lance Cpl. Daniel Smith, who is being detained inside the U.S. Embassy compound in Manila.
The acquittal came a few weeks after the victim recanted, saying the sex was consensual.
The mother of the woman said her daughter decided to change her story and left the country. The acquittal also came amid clamor for Smith to be turned over to Philippine authorities. A lower court sentenced Smith in December 2006 for the rape of the woman in a van at a former U.S. Navy base in Subic north of Manila. Three other defendants -- Lance Cpls. Keith Silkwood and Dominic Duplantis and SSgt. Chad Carpentier -- were all cleared of rape. The case has stirred strong protests from women's and left-wing groups in the Philippines and strained ties with the United States. The rape charges sparked a strong debate on whether an existing Visiting Forces Agreement between the United States and the Philippines should continue or be abrogated.