The left-handed Slovak, ranked nearly 100 places lower than Fognini, produced some thundering forehands and deft dropshots to run Fognini ragged on his way to a second ATP title.
Claycourt specialist Fognini, ranked 15 in the world, seemed to be cruising to his second title of the year in the opening set, whipping away baseline winners at will.
The tables were turned in the second set, however, with Fognini, who has already won the Vina del Mar tournament in Chile this year, feeling the full force of the 24-year-old Klizan's powerful forehand.
Klizan, who beat defending champion Tommy Haas in straight sets in the semis despite stomach pains, broke twice in the second set and continued to dominate in the decider, giving Fognini the run-a-round with a string of drop shots.
Fognini, renowned for his short temper, vented his frustration in the second game of the third set and was handed a point penalty after smashing his racket.
Klizan, whose ranking slumped after a wrist injury last year, kept his cool and never looked back.
"They can see my name now (on the winner's list). It was a crazy match today," Klizan, who played eight matches in nine days, said. "I was not very fit. I was just trying to fight and am very happy that I ended this tournament as champion."
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