Tsai led Chu by about 3 million votes in the poll, according to the island's election commission.
Tsai and her running mate Chen Chien-jen, got more than 6.89 million ballots, or 56.1 percent of the votes, whereas Chu and his running mate Wang Ju-hsuan, got more than 3.81 million ballots, or 31 percent of the votes.
PFP Chairman James Soong and his running mate Hsu Hsin-ying got nearly 1.58 million ballots, or 12.8 percent of the votes.
In a speech at the Kuomintang (KMT) headquarters in Taipei earlier, Eric Chu acknowledged his failure, saying he would take responsibility and resign from the post of KMT chairman.
Taiwan's legislature election was held simultaneously with the leadership election on Saturday.
Among the 113 seats in the island's legislature, DPP gained 68 seats while KMT got 35 and the New Power Party got five. Three seats went to the PFP, one went to the Non-Partisan Solidarity Union and one to independent candidate.