The World No. 6 Saina, who struggled with injuries this season, fought for 68 minutes before her Japanese rival got better of her.
Saina has been clubbed in Group B along with world No 1 and Olympic champion Li Xuerui of China, world No 7 Yeon Ju Bae of Korea, besides world No 13 Mitani during the December 11-15 year-end tournament, which is being fought among top eight performers from the 12-event Super Series circuit.
Top two players from Group A and B will advance to the semi-finals. The winner of Group A will play against the runner-up of Group B, while the winner of Group B take on the runner-up of Group A in the semi-finals for places in the final.
Saina hardly had to break sweat in the opening game. From being tied at 7-7, the Hyderabad-based shuttler opened a 12-7 lead and eventually wrapped it up 21-19 in style.
Saina began the second game also with a bang as she straightaway opened up a 7-0 lead. But the Japanese reduced it to 5-7 before making it 11-11.
Thereafter, it was a neck-and-neck battle and finally it was Mitani who stole the game to take the match it to the decider.
In the final game, Saina once again took an upper hand early on and always managed to maintain a slight lead but Mitani came from behind to make it 17-17.
At 19-19, Saina's poor fitness became a reason for her downfall as Mitani closed the match with couple of winners.
Image: Saina Nehwal
Photograph: Beawiharta/Reuters
Badminton rankings: Saina slips to seventh
Macau Open: Sindhu sizzles; lifts second Grand Prix Gold title
Saina, Sindhu lose in second round of French Super Series
Hong Kong Open: Saina wins first round; Kashyap, Sindhu exit
French Super Series: Saina, Sindhu advance; Jwala-Ashwini ousted