The fifth-seeded Indian squandered four match points to go down 21-15, 15-21, 20-22 to the third-seeded Okuhara in a match that lasted almost an hour. It was Saina's third successive defeat to the Japanese.
Going into the match with an overall 6-3 head-to-head count against Okuhara, Saina took time to get into the groove as Okuhra led 3-0 early on.
The Indian slowly clawed back at 6-6 before grabbing a slender 11-10 advantage at the first break.
After the interval, Saina continued to move ahead and reeled off five straight points at 15-12 to gain eight game points and soon pocketed the opening game.
In the second game, Okuhara again opened a 4-1 lead. She made it 6-6 but the Japanese broke off at 8-8 to make it 14-9 and then made rapid progress to roar back into the contest.
Saina stepped up in the decider, managing a 4-1 lead this time but Okuhara kept snapping at her heels, reducing the margin to 10-11 at the breather.
After the break, Saina produced five points on the trot to make it 16-10 and then grabbed four match points at 20-16.
But the Japanese dynamo showed her fighting spirit as she reeled off six points on the trot to surpass Saina and seal the match.
Saina had reached the final of the Indonesia Masters in January and the only tournament she won this year was the Commonwealth Games in April, beating compatriot P V Sindhu in the final at Gold Coast.
She also won a bronze at the 18th Asian Games.