The second-seeded Bouchard, who had not lost a set on the way to her second career final, held her nerve in the third set after five breaks of serve in a row to win in 1 hour, 53 minutes.
Pliskova beat top-seeded Angelique Kerber and No. 4 seed Elina Svitolina to reach the final and the Czech showed her fighting qualities after losing the opening set. But she was unable to claim her second career title after Kuala Lumpur in 2013.
The 20-year-old Bouchard had won the only previous matchup between the pair in the first round of the U.S. Open last year.