Klizan -- who reached the finals with a four-hour defeat of top seed Mikhail Youzhny in the semis -- needed only 69 minutes to down fourth-seeded Fognini 6-2, 6-3.
Klizan, ranked 45th and seeded third in St. Petersburg, closed the match by winning the final three games and had his service broken only twice during the contest.
He became the first Slovakian to win an ATP Tour event since Dominik Hrbaty in 2004.
Fognini fell to 0-2 in finals this season.
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