Hibino's speed on court caused problems for Vekic, who also appeared increasingly frustrated by the noisy crowd which frequently held up play in the capital of Uzbekistan.
The 21-year-old Hibino, ranked 117th in the world, held serve throughout and took advantage of nine double faults from Vekic to break her 19-year-old opponent twice in each set.
Hibino's only previous appearances in a WTA main draw came last month, when she reached the second round at the Japan Women's Open and Dalian Open. After wrapping up the win over Vekic, Hibino shook her head in disbelief and waved to supporters.
Vekic, who is ranked 137th after a disappointing season, drops to 1-3 in career WTA finals, with her last win coming at the 2014 Malaysian Open. It was her second appearance in a Tashkent final after losing in 2012 to Irina-Camelia Begu of Romania in straight sets.
Earlier Saturday, the Russian duo of Margarita Gasparyan and Alexandra Panova won the doubles final 6-1, 3-6, 10-3 against Russia's Vera Dushevina and Czech player Katerina Siniakova.