Klizan left center court briefly due to apparent stomach problems in the first set, but he rallied despite appearing to labor with continued difficulties to win in just under 90 minutes. He is the first qualifier to win an ATP World Tour title since Nicolas Mahut won the Topshelf Open in the Netherlands in June.
The 24-year-old Slovakian had lost his last three meetings with Fognini but he defeated the 15th-ranked Italian in his only previous final, at St. Petersburg in October 2012.
The 111-ranked Klizan defeated defending champion Tommy Haas in Saturday's semifinals, having already seen off the third-seeded and 2010 champion Mikhail Youzhny, as well as Denis Istomin -- who knocked out two-time former champion Philipp Kohlschreiber -- and Dudi Sela.
"Hopefully he's doing better now than he was during the match," Fognini said in comments reported by news agency dpa.
Asked if he thought Klizan had put on a show to throw him off, Fognini replied, "I think so. Let's see how many matches he's won in this manner at the end of the year."