The Higgins - a guided-missile destroyer - and the Antietam - a guided-missile cruiser - were sent as part of what has been seen as an attempt by Washington to counter efforts by Beijing to limit freedom of navigation in its waters.
China's Ministry of National Defense said the United States "seriously violated China's sovereignty" and undermined peace, security and mutual trust between the two nations and their militaries.
Washington has said it would like to see more global participation in its freedom of navigation operations in the South China Sea, through which about $5trn of ship-borne trade passes each year.
Woody Island in the Paracels is China's largest military outpost in the South China Sea, with more than 1,000 military personnel stationed on the island full-time.
The US military conducts what it calls "freedom of navigation" voyages in the South China Sea to contest Beijing's assertion of territorial rights in the area, although the US has no claims of its own in the disputed region.
The statement added that sucgh routine and regular operations "are not about one country, nor are they about making political statements".
USA officials accused Beijing of breaking a promise the Chinese leader, Xi Jinping, made in 2015 when he said China did not intend to militarise the disputed territories.
China's foreign minister said China had a right to take whatever measures it deemed fit on its island holdings, and the defence ministry criticized the USA move as "unconstructive", saying it would do nothing to change China's resolve to "play a role in maintaining peace and stability in the Asia-Pacific region".
In March, a U.S. Navy destroyer carried out a "freedom of navigation" operation close to Mischief Reef in the Spratly Islands.
'China's continued militarization of disputed features in the South China Sea only serves to raise tensions and destabilize the region, ' Pentagon spokesman Lieutenant Colonel Chris Logan said.
The United States has said it would like to see more global participation in freedom-of-navigation operations in the South China Sea.
"The United States naval vessels Antietam and Higgins entered without Chinese government permission into territorial waters" around the islands, which China calls the Xisha Islands, Mr Wu said in the statement.