The American is seeking her third WTA title after wins at Bogota in 2019 and Melbourne in 2022.
Navarro netted a forehand to surrender a break and a 5-2 lead in the final set to Anisimova, who closed with an ace to eliminate her compatriot in one hour and 55 minutes.
Anisimova, who ousted third-ranked Aryna Sabalenka in a quarter-final, will play for the title on Monday against the winner of a later semi-final between defending champion Jessica Pegula and 20-year-old left-hander Diana Shnaider.
Pegula is 2-0 against Anisimova, most recently winning in April at Charleston, while Shnaider has never played Anisimova.
It will be the fourth career WTA final for Anisimova, who dispatched her fourth top-20 foe of the week, a career first.
World number 15 Navarro also lost to Anisimova in their only prior meeting in 2022 at Indian Wells.
Anisimova took a nine-month mental health break from tennis last year and fell to 373rd in the world rankings at the start of the year, but has ensured a return to the top 50 in the next world rankings.
Third-seeded American Pegula, in her fourth consecutive Canadian semi-final, figures to be tested by Russia's 24th-ranked Shnaider, who ousted US top seed and reigning US Open champion Coco Gauff on Friday.
Shnaider comes off a silver-medal effort in doubles at the Paris Olympics and seeks her fourth WTA title of the year after Thailand, Bad Homburg and Budapest.
