World number six Berdych had been favourite to claim a first title on clay for five years but despite racing away with the opening set against 31-year-old journeyman Berlocq he fell to a disappointing defeat.
Like Berlocq, Klizan started as the underdog against enigmatic top seed Fognini and just like Berlocq also looked in danger of being swept aside.
However, the left-handed Slovakian, ranked 100 places below his opponent, hit back with thundering forehands and deft drop shots to leave Fognini reeling.
Claycourt specialist Fognini, ranked 15th 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, when Fognini felt the full force of the 24-year-old Klizan's game.
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."
With the French Open approaching no player is yet dominating on the clay with world number one Rafa Nadal struggling for form and Novak Djokovic battling a wrist injury.
Since the onset of the European claycourt season titles have been shared by the likes of Japan's Kei Nishikori, Bulgaria's Grigor Dimitrov and Swiss Stanislas Wawrinka, who beat Roger Federer in the Monte Carlo final.
(Reporting by Karolos Grohmann; Writing by Martyn Herman, editing by Ed Osmond)
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