Citing U.S. officials speaking on condition of anonymity, the newswire said USS John S. McCain sailed close to Mischief Reef in the Spratly Islands, an area which China is in a territorial dispute over with its neighbors.
The maneuvers came at a time when the U.S.is trying to secure China's help with reining in communist North Korea.
According to a US defense official, the USA destroyer was planning to sail within 6 nautical miles of Mischief Reef, one of Beijing's man-made islands.
But Washington's patrols have often angered Beijing because the United States is not a claimant in the territorial dispute in the mineral-rich South China Sea.
The whole territory of the South China Sea, which is believed to be extremely rich in energy resources, is disputed. It's true in the South China Sea.
"All operations are conducted in accordance with global law and demonstrate that the United States will fly, sail, and operate wherever worldwide law allows", she said.
The building of military and dual-use infrastructure on the three biggest islands in the contested Spratly chain - Mischief, Subi and Fiery Cross reefs - has reached the final stages, with naval, air, radar and defensive facilities largely complete, the report said.
"They happen off the coast of Canada" and "in the waters off shore of our major allies, friends, partners all around the world", she said.
Geng said the Chinese navy "identified the USA warship, warned and expelled it".
China has territorial disputes with its neighbours over the area. US President Donald Trump and his administration have been pressing China to exert more economic and diplomatic pressure on the isolated North Korean regime to prevent tensions from escalating further in the Korea peninsula. Beijing called the move a "serious political and military provocation".
China's foreign ministry said the operation had "violated global and Chinese law and seriously harmed Beijing's sovereignty and security".
Attracted by the strategic military location and the prospect of oil, China, Taiwan, Brunei, the Philippines, Malaysia and Vietnam have all laid territorial claim to the Spratly's and have occupied several islands.