The third-seeded Klizan broke the fourth-seeded Fognini twice in the first set and four times in the second. The last break came in the final game, when the left-hander hit a cross-court forehand winner to seal the victory.
Klizan had used his only ace of the match to close out the first set.
In the past seven months, the 23-year-old Slovak has moved up from No. 121 in the world to a career-high 45th. His breakthrough season included reaching the fourth round of the U.S. Open by beating No. 6-ranked Jo-Wilfred Tsonga.
Fognini, ranked 53rd, was playing in his second ATP final but is still looking for his first title.
Klizan reached the final in St. Petersburg by upsetting top-seeded Mikhail Youzhny of Russia in a three-set match that lasted nearly four hours Saturday. After a short break, Klizan played a doubles semifinal, which he and his partner lost.
"I was really dead yesterday after the match, but I played very solid this week and I'm very happy that I won this week," Klizan said. "It's my first title and I hope not last, and I hope I can make more points in the end of this season."