USA officials, speaking on condition of anonymity, said the Higgins guided-missile destroyer and the Antietam, a guided-missile cruiser, came within 12 nautical miles of the Paracel Islands.
On May 18, China announced that it had for the first time landed its H-6K strategic bomber on an outpost in the Paracels, Woody Island.
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters.
The U.S. military did not directly comment on Sunday's operation, but said U.S. forces operate in the region daily.
The U.S. Department of Defense cited China's moves to militarize the Spratly Islands, where it has constructed seven artificial islands, as a reason for the disinvitation.
These operations "are not about one country", he said, "nor are they about making political statements".
China now asserts its right to the islands.
China's military, he said, would be "firm and unwavering in its determination to strengthen sea and air operational preparedness construction" on the islands.
US sends warships near disputed island in South China Sea: report | TheHill
"We conduct routine and regular Freedom of Navigation Operations (FONOPs), as we have done in the past and will continue to do in the future", said the United States Pacific Fleet, according to the news service.
The move has been conducted several times in the past three years in defiance of China's claims it owns the disputed territory.
A US Navy soldier stands aboard the USS Higgins destroyer.
American warships will continue to be deployed in the region "on an everyday basis", Pentagon spokesman Lt. Col. Christopher Logan told the Russian media on Sunday.
Its neighbours, particularly some of those involved in maritime disputes over the waters, have expressed fears China could eventually restrict freedom of navigation and overflight.
China's military took "immediate action" on Sunday against "unauthorized" sailing by U.S. warships in South China Sea waters claimed by Beijing.
"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.
Du Plessis blitz puts Chennai in IPL final
While all the batsmen of Chennai Super Kings failed to perform yesterday, the innings of opener Faf du Plessis was outstanding. In the ninth over, in the first show of aggression, he deposited a short delivery from Brathwaite into the stands.