China will see the move as a Donald Trump’s nation giving backing to Taiwan over the ongioing dispute.
Beijing sees Taiwan as a rogue province and has continued to flex authority over the self-ruling state.
However, Commander Nate Christensen, deputy spokesman for US Pacific Fleet, said in a statement: “The ships’ transit through the Taiwan Strait demonstrates the US commitment to a free and open Indo-Pacific.
“The US Navy will continue to fly, sail and operate anywhere international law allows.”
US Navy warships carried out a similar move in July which sparked anger in Beijing.
The latest mission saw two warships pass through the Taiwan Strait earlier today.
US officials had warned on Saturday they were considering a move to send a message to ensure free passage through the waterway.
The Pentagon had said China’s navy had shown “unsafe and unprofessional” conduct in the region after a Chinese destroyer moved close to an American warship earlier this week.
Kelsey Broderick, an associate for Asia at Eurasia Group in Washington, warned the move was likely to infuriate Beijing.
He said: “China would view a US naval exercise of this magnitude in its territorial waters as a significant provocation, likely further cutting off mil-to-mil contact.
“It would also empower the hardliners in China that view the U.S. as committed to containing China economically and militarily – making a settlement on the trade dispute even more unlikely in 2018.”
The waters in the South China Sea and Taiwan Strait has been disputed regions between the world super powers for some time.
Beijing has been ramping up pressure to assert its sovereignty over the island.
Taiwan’s foreign ministry declined comment.
Taiwan’s relations with China have deteriorated since the island’s President Tsai Ing-wen from the independence-leaning Democratic Progressive Party swept to power in 2016.
This year, China increased military and diplomatic pressure, conducting air and sea military exercises around the island and persuading three of the few governments still supporting Taiwan to drop their backing.
Tsai said earlier this month she will maintain the status quo with Beijing, but also vowed to boost Taiwan’s national security and said her government would not submit to Chinese suppression.