Fujino, who led after the opening round, offset three bogeys with three birdies at the Ryukyu Golf Club to finish with a 1-over 217 total.
Defending champion Ai Miyazato, who led Japan to victory at last month's inaugural Women's World Cup, had back-to-back 75s in the first two rounds and could only manage a 4-over 76 on the final day for a share of 27th place at 10-over 226.
Overnight leader Michiko Hattori closed with a 74 on Sunday to finish one stroke behind Fujino.
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