The ninth-seeded Stakhovsky bounced back after dropping the first set, prevailing in a 3-6, 6-3, 6-4 decision over the 15th-seeded Istomin.
After the Uzbek charged out of the gate to post a convincing first-set win, Stakhovsky turned it on and wasn't seriously challenged again.
In the final set, Istomin lost his third service game and Stakhovsky held at love on his next two serves. Then, at 40-30 leading 5-4, he hit an overhead winner to take the championship.
Stakhovsky won his second crown of the year after a victory in Den Bosch. He has never lost a final.
Istomin was appearing in his first career final and fell short in his bid to become the first Uzbek to win an ATP event.