She had a smooth run through the semifinals but probably the pressure of gold medal match got to her against fourth-seed Li Jiaman, a team silver medalist from the Paris Olympics.
It was Deepika's ninth appearance at the World Cup Final where she has also bagged a bronze.
Dola Banerjee is the only Indian archer to have won a gold in the World Cup Final, having topped the podium in Dubai 2007.
In the men's recurve section,
The pressure once again seemed to affect the Indian archers, who have often struggled in high-stakes matches.
The five-member Indian contingent, comprising three compound and two recurve archers, thus concluded their season-ending World Cup Final campaign with just one medal.
After a stellar semifinal win against Mexico's Alejandra Valencia, Deepika couldn't maintain momentum.
She dropped the first set by a single point (26-27). Despite improving in the second set, Li's flawless 30, including an X-ring shot, gave the Chinese archer a commanding a 2-0 lead (30-28).
The third set proved decisive as Deepika's second arrow landed in the red 7-ring, allowing Li to claim victory with three solid 9s, taking the set 27-25 and sealing the gold on her debut World Cup Final appearance.
In the semifinals, Deepika triumphed over home favourite and Paris Olympics bronze medalist Valencia, edging her out 6-4 (29-28, 26-26, 26-29, 28-28, 28-27). It also avenged Deepika's bronze medal loss to Valencia from the Yecheon World Cup earlier this year.
Deepika's campaign had begun with a dominant 6-0 victory over China's Yang Xiaolei (27-23, 29-22, 29-27).
In the men's recurve, third-seeded Dhiraj was India's sole qualifier.
Facing second seed Lee Woo Seok, Dhiraj started strongly, drawing the first set and winning the second.
However, he missed the opportunity to close out the match in the third by just one point with the South Korean drawing level before delivering flawless performances in the fourth and fifth sets.
Dhiraj eventually lost 4-6 (28-28, 29-26, 28-28, 26-30, 28-29).
On the compound side, the three-member Indian contingent returned empty-handed ending their campaign on Saturday.
Prathamesh Fuge finished fourth after a tense semifinal loss, while Priyansh and Jyothi Surekha Vennam failed to reach the medal rounds.