Lance Corporal Devin Jacob Ballard, 20, is suspected of killing Anna Yagi, 39, in a hotel in Naha, the capital of the southernmost prefecture, on Saturday and taking her wallet and backpack. Ballard denied the allegations, police said.
The case is the latest in a string of incidents stretching back years that have fuelled unease over the large US troop presence on the island chain near Taiwan and China, with US officials warning it could undermine ties vital to security in East Asia.
"Every interaction with our neighbours either builds or undermines the trust that is essential to our team. When that trust is damaged, it affects the strength of our alliance and the security of this region," Lieutenant General Benjamin Watson said in a statement on Tuesday ordering the measures.
All US military operations on Okinawa would be paused for 48 hours while troops underwent training on standards and discipline, Watson said.
Prime Minister Sanae Takaichi called Saturday's killing "extremely brutal and heinous".
She said she had strongly protested to the US and demanded measures to prevent such incidents in the future.
Yagi died of asphyxiation after Ballard allegedly "pressed on her neck", police told the Stars and Stripes newspaper.
Hotel staff found the woman unconscious in her room in the early hours of Saturday after she failed to check out.
About 200 officers were involved in a search for the man earlier caught on CCTV entering the hotel with the victim, local media reported.
In a meeting with Okinawa Governor Genta Koja in Tokyo, Takaichi said Japan and the US would continue to consult on effective measures to prevent such incidents from occurring.
The incident sparked protests in Naha and Tokyo.
Japan hosts the largest overseas contingent of US forces globally. Most of the 18,000 Japan-based Marines are stationed in Okinawa, which the US held from the end of World War II until 1972.
That presence has repeatedly stirred resentment among residents over issues such as noise, aircraft crashes and the conduct of personnel.
The 1995 rape of a 12-year-old Okinawan girl by three US servicemen sparked mass demonstrations.
Saturday's killing could complicate Takaichi's efforts to relocate some Marines from the busy Futenma air base to a more remote facility at Henoko.
Opponents want the troops moved out of the prefecture.
Okinawa, which is 100km from Taiwan at the closest point, is viewed by Tokyo and Washington as key in deterring potential military aggression from China.
