A U.S. defense official told CNN that the destroyer USS Lassen "conducted a transit" within 12 nautical miles of Subi Reef in the Spratly Islands on Tuesday morning local time.
The operation put the ship within an area that would be considered Chinese sovereign territory if the U.S. recognized the man-made islands as being Chinese territory, the official added.
The mission, which had the approval of President Barack Obama, has now concluded, the official said.
The United States had not breached the 12-mile limit since China began massive dredging operations to turn three reefs into artificial islands in 2014.
In little more than 18 months, China has reclaimed more than 2000 acres at three main locations in the Spratly Islands -- Subi, Mischief and Fiery Cross reefs.
The South China Sea is the subject of numerous rival
and often messy territorial claims, with China, Brunei, Malaysia, the Philippines, Taiwan and Vietnam disputing sovereignty of several island chains and nearby waters.
On Tuesday morning before it was confirmed that the U.S. warship had breached the 12-mile zone, Wang Yi, China's foreign minister, said:
"We advise the U.S. side to think twice before action, not to conduct any rash action, and not to create trouble out of nothing."
China has repeatedly said its activity in the South China Sea does not target any other country or affect freedom of navigation by sea or air.
Another defense official told CNN that the operation was "routine" and was in accordance with international law.
"We will fly, sail and operate anywhere in the world that international law allows," the official said.
"U.S. Freedom of Navigation operations are global in scope and executed against a wide range of excessive maritime claims, irrespective of the coastal state advancing the excessive claim," the official added.
His comments echoed those of State Department spokesman John Kirby on Monday, who said one country didn't need to consult another "when you are exercising the right of freedom of navigation in international waters."
Zhu Haiquan, the spokesperson of the Chinese Embassy in Washington said: "Freedom of navigation and overflight should not be used as excuse to flex muscle and undermine other countries' sovereignty and security."
"We urge the United States to refrain from saying or doing anything provocative and act responsibly in maintaining regional peace and stability," Zhu said in a statement Monday night.
The rest of the region, wary of China's intentions in the disputed waters, are likely to welcome the U.S. move.
Japan's Chief Cabinet Secretary Yoshihide Suga declined to comment on the operation but said "it was extremely important that the international community work together in order to protect open, free and peaceful ocean."
The United States has called for an immediate halt to China's island building in the South China Sea.
China said in June that land reclamation was "almost complete," although it did say that it would continue to build facilities on the islands it has already created.
News of the ship's plan was first reported by Reuters
Chinese navy ships entered U.S. territorial waters off Alaska in September, coming within 12 miles of the coastline during President Barack Obama's visit
to the state, U.S. officials told CNN at the time.
The officials emphasized that China's actions were consistent with "innocent passage" under international maritime law.
Greg Poling, director of the Asia Maritime Transparency Initiative
at the Center for Strategic and International Studies in Washington said that the U.S. operation was aimed at testing control of the seas, not sovereignty over the disputed islands and would present a dilemma for China.
"It forces a clarification of China's claims. China's strategy in the South China Sea is one of ambiguity," he said.
Poling said under maritime law, artificial islands were not usually afforded the 12-mile territorial zone, and that the U.S. Navy deliberately chose to send the destroyer near Subi Reef for this reason.
Before China's recent land reclamation, both Subi and Mischief reefs were submerged at high tide, while a sandbar was visible at high-tide at Fiery Cross Reef, which could make its legal status more ambiguous.
"So if Beijing objects by saying to the U.S. you're in our territorial sea, then the U.S. respond can respond by saying there's no such thing as a territorial sea for an artificial island," Poling said.
He said that the decision to go ahead with the mission follows months of discussion in Washington and likely followed Chinese President Xi Jinping's trip to Washington last month, which made little headway on the South China Sea.