China claims democratically-ruled Taiwan as its own territory, and has mounted repeated air force missions into Taiwan's air defence identification zone (ADIZ) over the past year, provoking anger in Taipei.
China sent around 150 aircraft into the zone over a four-day period beginning on Oct. 1 in a further heightening of tension between Beijing and Taipei that has sparked concern internationally.
The US military said the Arleigh Burke-class guided missile destroyer USS Dewey sailed through the narrow waterway that separates Taiwan from its giant neighbour China along with the Canadian frigate HMCS Winnipeg on Thursday and Friday.
"Dewey's and Winnipeg's transit through the Taiwan Strait demonstrates the commitment of the United States and our allies and partners to a free and open Indo-Pacific," it added.
China's People's Liberation Army's Eastern Theatre Command said its forces monitored the ships and "stood guard" throughout their passage.
"The United States and Canada colluded to provoke and stir up trouble... seriously jeopardising peace and stability of the Taiwan Strait," it said.
"Taiwan is part of Chinese territory. Theatre forces always maintain a high level of alert and resolutely counter all threats and provocations."
US Navy ships have been transiting the strait roughly monthly, to the anger of Beijing, which has accused Washington of stoking regional tensions. U.S. allies occasionally also send ships through the strait, including Britain last month.
While tensions across the Taiwan Strait have risen, there has been no shooting and Chinese aircraft have not entered Taiwanese air space, concentrating their activity in the southwestern part of the ADIZ.
While including Taiwanese territorial air space, the ADIZ encompasses a broader area that Taiwan monitors and patrols that acts to give it more time to respond to any threats.
Taiwan's defence ministry said on Sunday that three Chinese aircraft - two J-16 fighters and an anti-submarine aircraft - flew into the ADIZ again.