The call, confirmed by four people, is believed to be the first between a US president or president-elect and a leader of Taiwan since diplomatic relations between the two were cut in 1979.
Although it is not clear if the Trump transition team intended the conversation to signal a broader change in US policy towards Taiwan, the call is likely to infuriate Beijing which regards the island as a renegade province.
The US has adopted the so-called "One China" policy since 1972 after the Nixon-Mao meetings and in 1978 President Jimmy Carter formally recognized Beijing as the sole government of China, with the US embassy closing in Taipei the year after.
The Trump team did not initially respond to multiple requests for comment but, after the Financial Times first published news of the call, confirmed that the president-elect had spoken with Ms Tsai and "noted the close economic, political, and security ties" between Taiwan and the United States.
"The Chinese leadership will see this as a highly provocative action, of historic proportions," said Evan Medeiros, former Asia director at the White House national security council, who now heads Asia research at Eurasia Group.
"Regardless if it was deliberate or accidental, this phone call will fundamentally change China's perceptions of Trump's strategic intentions for the negative. With this kind of move, Trump is setting a foundation of enduring mistrust and strategic competition for US-China relations."
Douglas Paal, who as head of the American Institute in Taiwan from 2002 to 2006 was the de facto US ambassador, said that he was not aware of any such telephone calls between US and Taiwanese presidents since 1979.