It was the latest move by the Communist state to bolster its claims in the strategic waterway that China claims as its own.
The Obama administration warned Trump's call with Taiwan could undermine progress in relations with Beijing.
Trump's transition team doubles down on Taiwan call, terming it a "courtesy."
'This was a courtesy call. The democratically elected president of Taiwan called to congratulate the president-elect,' the vice president-elect says.
Senator Chris Murphy tweets Trump's actions are 'major pivots in foreign policy' without planning, which is 'how wars start.'
Chinese officials lodge 'stern representations' with the 'relevant U.S. side' but blame Taiwan for the diplomatic breach.
The call was the first such contact with Taiwan by a U.S. president-elect or president since President Jimmy Carter adopted a one-China policy in 1979.
More than 50 people in the city state have been infected with the mosquito-borne virus.
The streaming video service has footholds in Taiwan, Hong Kong and Macau, but mainland China, and its vast potential, is much harder to penetrate.
Security experts have warned this could be the first of many military flights.
U.S. officials, speaking on condition of anonymity, identified the suspect as Lieutenant Commander Edward Lin.
From marches to concerts, how the world will commemorate the day.
The U.S. says it will continue conducting "freedom of navigation patrols" by ships and aircraft to assure unimpeded passage through the region.
His one-day visit comes amid growing international concern over rising tensions in area.
Tens of thousands of tourists have also been stranded, as snow grounds flights.
But the independence-leaning opposition leader Tsai Ing-wen also vows to defend Taiwan's sovereignty.
The U.S. wants to see issues between the two dealt with peacefully, no matter who wins Saturday's polls.
Beijing didn't have regular diplomatic relations with pro-Western Seoul until the 1980s.
Chan is close to China's communist party and has called Taiwanese democracy "a joke."