The Hyderabad girl scored an upset 5-7 6-4 6-4 win over her rival from Maharashtra, who is ranked 400th in the world, in three hours and 15 minutes to dash Prarthana's hopes of completing a double crown in the tournament.
Prarthana started well by breaking her rival's serve in the 12th game to clinch the opening set 7-5.
Some intelligent play by Sowjanya helped her in the second set, when the score was 4-4. She saved two break points to hold her serve and go up 5-4 and then broke Prarthana in the 10th to clinch it 6-4 and draw level in the match.
Emboldened by her comeback, Sowjanya broke the second seed at love in the 10th game to win the set as well as her second ITF title, and the first at home.
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"I'm just thrilled and can't say much now, the ninth game in the decider made all difference to my confidence and I knew I got it (right) mentally," said Sowjanya, who got 12 WTA points and USD 1,560 for her effort.
On her way to the title Sowjanya had defeated no. 4 seed Emi Mutaguchi of Japan, no. 6 Prerna Bhambri and Prarthana.
Prarthana had won the doubles title yesterday with singles top seed Ankita Raina.