Playing her second final in two weeks, world number three Saina could not live upto expectations against 21-year-old Minatsu and lost 19-21 11-21 in the 39-minute women's singles final.
Saina, who won the Denmark Super Series Premier title last week, was tested only for the second time in the tournament by world number 26 Minatsu, who rode on her superior court coverage and accurate strokes to clinch her first Super Series title.
Minatsu, who jumped a couple of places in world rankings on Thursday, matched Saina with her brilliant net play and smashes and engaged the Indian in long rallies. She was also good in her defence as she retrieved everything thrown at her.
Saina started off well and initially opened up a narrow 6-3 lead but Minatsu slowly built her game and moved from 7-7 to 16-16 to keep breathing down the Indian's neck.
The 22-year-old from Hyderabad picked up a couple of points to move to 18-16 but the Japanese reeled off four straight points from 17-19 to to win the first game.
In the second game, Saina tried to exploit Minatsu's weakness at the fore court and played some angled shots to move to 5-2.
But Minatsu engaged Saina in long rallies and used her drops and cross court smashes to catch up with the Indian, before moving into the break at 11-10 with yet another brilliant smash. She grabbed four more quick points to move to 15-10.
Minatsu made Saina move around the court by mixing her shots, while the Indian faltered with her accuracy and lost a few points hitting wide or due to misjudgement. In no time, Minatsu zoomed to match point at 20-11 and with Saina finding the net, it was all over for the Indian.