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Trump's spokesperson Hope Hicks confirmed the phone call in an email on Friday.
"President-elect Trump spoke with President Tsai Ing-wen of Taiwan, who offered her congratulations," according to a readout of the call released by Trump's transition team.
"During the discussion, they noted the close economic, political, and security ties exists between Taiwan and the United States. President-elect Trump also congratulated President Tsai on becoming President of Taiwan earlier this year."
The call is the first time a US president has directly spoken with Taiwan's leadership in more than 30 years. The US suspended formal diplomatic relations with Taiwan in 1979 after establishing a One China position in an effort to establish diplomatic channels with Beijing.
"The United States of America acknowledges the Chinese position that there is but one China and Taiwan is part of China," the One China principle states.
Meanwhile, the Republic of China, the formal name for Taiwan, holds that a concensus was reached in 1992 between the Chinese Communist Party and the party ruling Taiwan at the time which slightly normalized relations and established Taiwan as a distinct system.
Analysts were quick to point out that the phone call will likely infuriate Beijing.
"Trump has phone call w Taiwan President, 1st by US Pres or Pres-elect since 1979," goepolitical expert Ian Bremmer, president of Eurasia Group, tweeted on Friday. "Beijing will be absolutely incensed."
"Trump almost surely unaware of Taiwan-China sensitivities before taking President's call," Bremmer added. "They don't yet have Asia expertise on team."
Evan Medeiros, former Asia director at the White House national security council, told the Financial Times "the Chinese leadership will see this as a highly provocative action, of historic proportions."
"Regardless if it was deliberate or accidental, this phone call will fundamentally change China's perceptions of Trump's strategic intentions for the negative," he said. "With this kind of move, Trump is setting a foundation of enduring mistrust and strategic competition for US-China relations."
Trump has apparently been considering building a luxury hotel chain in the northwest Taiwanese city of Taoyuan, the Shanghaiist reported last month.
Henry Kissinger - who, as Secretary of State, arranged Nixon's initial trip to Beijing to establish ties in 1972 - is currently visiting Beijing. Kissinger met with Trump at Trump Tower after the election and told reporters that Trump "has absolutely no baggage."
"He has no obligation to any particular group because he has become a president on the basis of his own strategy and a program he put before the American public that his competitors did not present," Kissinger said. "So that is a unique situation."
Ying-wen, the Taiwanese president, reportedly congratulated Trump on his win, and said she looks forward to working with him.