The third-seeded Hantuchova was defeated in the first set by the fourth-seeded Kirilenko, but rallied to take the next two in a 6-7 (4-7) 6-3, 6-3 victory.
The Australian Open runner-up, Hantuchova fired six aces and won 69 percent of her first serve points as the Slovakian won her fifth WTA title. She beat Tamarine Tanasugarn last year in the final at this event.
The 20th-ranked Hanutchova improved to just 5-9 all-time in WTA finals while Russia's Kirilenko fell to 5-5.
The 26th-ranked Kirilenko hasn't won a final since a victory over Samanha Stosur in Seoul in September 2008.
Hantuchova improved to 5-2 lifetime against Kirilenko and this was the first time the two met in a final.
Hantuchova collected $37,000 for the victory.