Skyler Dozierwalker, 23, and Christopher Browning, 24, attacked the woman in central Okinawa during a brief trip to the semi-tropical island chain.
Dozierwalker told Naha District Court he committed the crime, while Browning also admitted the charges but denied having conspired with the petty officer in advance, Jiji Press and Kyodo News said.
Okinawa is the reluctant host of more than half of the 47,000 US military personnel in Japan. The rape provoked outrage and led to a nationwide curfew on all American military personnel in Japan.
Despite the curfew, misconduct involving US servicemen, much of it drunken, has continued to fuel anti-US sentiment in communities with bases.
The attack came amid already high tensions in Okinawa, which saw demonstrations last year against the US deployment to the island of Osprey aircraft. Local activists charge they have a poor safety record.
In 1995 the gang rape of a 12-year-old Okinawan girl by US servicemen sparked mass protests resulting in a US-Japan agreement to reduce the huge US military presence on the Okinawan chain.
Washington sees the island as a vital strategic base in a region that is increasingly wary of the power of China's rising military.
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Rape is apparently not an uncommon problem among the US military. They rape their own comrades, male and female, so why not others... disgusting.... don't know the numbers on other countries' armies, but I know the US is not doing nearly enough to prosecute those responsible. However with recent public outcry and bad press (watch the documentary The Invisible War) that may finally change.