A guided-missile destroyer and guided-missile cruiser both made the politically sensitive trip, the first such voyage by U.S. vessels since July.
The Defense Department declined to say the move was a signal to China, but rather that it demonstrated a US commitment to a "free and open" Indo-Pacific.
The U.S. Navy sailed two warships through the Taiwan Strait for the second time since July, a show of force that threatens to further exacerbate tensions with China.
Two U.S. defense officials told CNN that several Chinese warships followed the Yokosuka-based 7th Fleet ships at a safe distance.
Beijing "expressed its concern to the U.S. side" as "the Taiwan issue concerns China's sovereignty and territorial integrity", Chinese foreign ministry spokeswoman Hua Chunying told a regular news briefing.
"The Taiwan question bears on China's sovereignty and territorial integrity and it is the most important and sensitive issue in China-U.S. relations", Foreign Ministry spokeswoman Hua Chunying said at the time, warning the Americans against actions that would "undermine China-U.S. ties and the peace and stability across the Taiwan Strait".
The USS Curtis Wilbur and USS Antietam conducted a routine transit on Monday to demonstrate US commitment "to a free and open Indo-Pacific", Commander Nate Christensen, deputy spokesman for US Pacific Fleet, said in a statement.
"The DOD will continue to fly, sail, and operate wherever worldwide law permits", said Pentagon spokesman Army Col. Rob Manning. Taiwan receives support and defense funding from the United States in line with a 1979 bilateral agreement. -China relationship continues to be USA support for Taiwan. The U.S. has also accused China of engaging in cyberattacks against the U.S. government and businesses.
China has become increasingly aggressive in the Taiwan Strait towards Taiwan, which China considers a renegade province and not a separate country.
It has also viewed US overtures toward Taiwan with alarm, including its unveiling a new de facto embassy in Taiwan and passage of the Taiwan Travel Act, which encourages USA officials to visit the island.