Japan’s largest ship, the helicopter carrier Kaga, and two destroyers, conducted drills in recent days with the Ronald Reagan aircraft carrier strike group.
Vietnam and other claimants to disputed territory in the waters have been watching with growing alarm as Beijing steps up militarisation of the strategic waterway, and the US counters with increased naval patrols and exercises.
The Japanese task force is conducting a rare month long tour of the region, an assertion of Tokyo’s determination to stand up to China’s ever more assertive claims to the waters off its southern and eastern coasts.
The joint exercise with US ships in the South China Sea risks provoking a further escalation from China which claims historic ownership of the waters.
Beijing is particularly sensitive to any challenge from Japan, given the historical enmity between the two powers and their separate standoff over disputed islands in the East China Sea.
The United States has already received support from other allies, including Australia, France and Britain, which have sent warships on “freedom of navigation” missions through the disputed waterway.
Last week, B52 heavy bombers from Guam flew over the area in support of the allied naval manoeuvres.
Vietnam has also been building up defences on its islands in the disputed Spratly chain, but on a far more modest level than China which has built sprawling new military bases on reclaimed land.
Hanoi recently expressed pleasure at signs of limited progress in the glacially slow efforts by China and ASEAN to agree a code of conduct to reduce the risk of conflict in the disputed waters.
Analysts caution, however, that the negotiations are likely to remain a sideshow while the superpowers flex their military muscles and build up their strike capabilities.
China has conducted eight military drills in the South China Sea this year alone, dispatching its first aircraft carrier in a show of force designed to underline its determination to stay put.
Chinese leaders no longer pay lip service to their earlier denials that they would militarise the area.
The official Chinese line now is that the military buildup is for defensive purposes given the challenge posed by the US and its partners.
In recent months, China has landed bombers on its outposts on the Paracel Islands, which are also claimed by Vietnam, and has fortified its new bases with radar and missile systems.
China frequently challenges US aircraft and naval vessels as they conduct their operations over what are legally international waters.
The fear is that one such confrontation could get out of control and lead to a rapid escalation.