Opposition Democratic Progressive Party candidate Tsai ousted the ruling Kuomintang to take the presidency yesterday as voters turned their backs on closer ties with China.
Tokyo hailed her achievement in a statement which also paid tribute to the island's democracy.
"The government of Japan congratulates Ms Tsai on her victory, and praises the smooth implementation of the election which demonstrates that democracy in Taiwan has deeply taken root," Foreign Minister Fumio Kishida in a statement issued late yesterday.
Beijing responded sternly to Tsai's election, with foreign ministry spokesman Hong Lei warning that "the Chinese government is rock-firm and will never tolerate any secessionist activity of 'Taiwan independence'".
Kishida only said Japan hoped the issues surrounding Taiwan would be "resolved peacefully".
"We expect that the issue surrounding Taiwan will be resolved peacefully by direct dialogue between the concerned parties and that it will contribute to the peace and stability of the region," he said.
