The USS Hopper came within 12 nautical miles of Huangyan Island on Wednesday, China’s foreign ministry stated.
The small island, also known as the Scarborough Shoal, is a disputed territory also claimed by the Philippines.
The US has slammed China for constructing islands and military installations in the region, arguing they could be used to obstruct free trade routes.
American officials, speaking to Reuters on condition of anonymity, have said Wednesday’s “innocent passage” patrol was in accordance with international law.
Twelve nautical miles is the territorial limit recognised internationally.
Chinese foreign ministry spokesman Lu Kang said the ship violated his country’s sovereignty and security interests.
He added that it threatened the safety of the nation’s ships and navy personnel in the waters.
China’s navy ordered the vessel to withdraw after determining its identity.
The US military has a longstanding position that such operations are carried out throughout the world, including in areas claimed by allies, and that they are separate from political considerations.
In a statement, the Pentagon did not directly comment on the patrol but said the United States routinely carries out “freedom of navigation” operations, a summary of which would be released in an annual report.
Mr Kang added that China “firmly opposes” efforts to use freedom of navigation as an excuse to hurt its sovereignty and urged the United States to “correct its mistakes.”
Pentagon spokesman Lieutenant Colonel Christopher Logan said: ”All operations are conducted in accordance with international law and demonstrate that the United States will fly, sail, and operate wherever international law allows.”
In a separate statement on Saturday, China’s defence ministry said the repeated dispatch of US warships to the region was “undermining regional peace and stability” and hurting bilateral relations.
US President Donald Trump is seeking the support of the Chinese in dealing with North Korea’s nuclear and missile programs.