Shnaider had little trouble in the opening set but struggled in a topsy-turvy second, as Alexandrova clinched the set's fifth and decisive break at 5-4 to force a decider.
Third seed Shnaider carved out an advantage early on in the third set when she broke Alexandrova in the first game and held serve to go 2-0 up, an advantage she would not relinquish.
World No. 12 Shnaider is now unbeaten in her last five finals on the WTA Tour, adding the Monterrey crown to her triumphs in Hong Kong, Budapest, Bad Homburg, and Hua Hin last year.
The win also saw Shnaider level her head-to-head record with Alexandrova, who was faced with a quick turnaround for the final after her semi-final against Czech Marie Bouzkova was moved from Friday to Saturday due to a rain-enforced suspension.
Both players will have little time to rest after the final before they make the nearly 2,000-mile journey from Monterrey to New York to play in the first round of the U.S. Open, which begins on Sunday.
Shnaider will face Germany's Laura Siegemund, while Alexandrova takes on Anastasija Sevastova of Latvia.