"This operation challenged attempts by the three claimants, China, Taiwan and Vietnam, to restrict navigation rights and freedoms around the features they claim by policies that require prior permission or notification of transit within territorial seas," Cmdr. Bill Urban said.
"This operation demonstrates, as President Obama and Secretary [Ash] Carter have stated, the United States will fly, sail and operate anywhere international law allows. That is true in the South China Sea, as in other places around the globe."
The USS Curtis Wilbur, an Arleigh Burke-class guided missile destroyer, sailed within 12 nautical miles of the Triton Island, part of the Paracel Islands -- an archipelago claimed by the three.
None of them was notified of the move.
"This operation was about challenging excessive maritime claims that restrict the rights and freedoms of the United States and others, not about territorial claims to land features," Urban said. "The United States takes no position on competing sovereignty claims between the parties to naturally formed land features in the South China Sea. The United States does take a strong position on protecting the rights, freedoms, and lawful uses of the sea and airspace guaranteed to all countries, and that all maritime claims must comply with international law."
A spokeswoman for China's Foreign Ministry denounced the action.
"The U.S. naval ship violated Chinese law to enter China's territorial waters. China monitored the ship's movement and issued verbal messages in accordance with law," Hua Chunying said. "We urge the U.S. side to respect and abide by relevant laws of China, and do more to improve mutual trust as well as regional peace and stability."
Cui Tiankai, the Chinese ambassador to the United States, told CNN's Christiane Amanpour that the operation was "a very serious provocation, politically and militarily."
And a spokesman for the Chinese defense ministry, Senior Col. Yang Yujun, said Saturday's move and ones like it are "very unprofessional and irresponsible in terms of the safety of troops on both sides."
"It may cause extremely dangerous consequences," Yang said. "No matter what provocative actions the U.S. takes, the Chinese military will take all necessary means to firmly protect sovereignty and security."
The U.S. conducted a similar operation in October. China said it warned that warship, the USS Lassen, as it came close to reefs claimed by China in contested waters.
Much of the South China Sea is subject to a series of territorial disputes between Asian nations.
And near the Spratly Islands, which Beijing calls the Nansha islands, China has built an artificial island with air strips that analysts believe will be able to accommodate bombers.
Explaining the South China Sea dispute
