The world number 23 triumphed 5-7, 7-6 (7/4), 6-3 to add the Czech trophy to her victory in Tallinn last weekend.
Krejcikova's success snapped French and US Open champion Swiatek's 10-final win streak and gave the Czech a fifth career singles title.
Swiatek, who had racked up her 60th win of the season on Saturday, went into Sunday's final having won both her previous meetings with Krejcikova.
The Pole won in straight sets on the hard courts of Miami last year before a three-set victory on the clay of Rome two months later.
On Sunday, Krejcikova took the tough route to victory having trailed 5-1 in the opening set before battling back to claim the match in three hours and 16 minutes.
For Swiatek, it was just her second career defeat in 12 finals, and first in three years.
