The sixth-seeded Youzhny broke unseeded Haase's service once in each set to clinch his ninth career title, and third on clay courts.
A former top-10 player now ranked No. 33, the 31-year-old Russian had never previously reached the final at Gstaad in seven visits since 2002.
Youzhny improved his record to 5-0 against the 57th-ranked Dutchman.
"I never beat you and it kind of hurts, but you deserved it," Haase said in an on-court interview.