Yuika Sugasawa also converted a penalty as the Nadeshiko closed on qualifying for the last 16, just four days after a disappointing display in a goalless draw against outsiders Argentina.
Asako Takakura's team, ranked seventh in the world, will now go into their final Group D game against England next week with a chance of topping the section, which would ensure a far more favourable draw in the last 16.
Scotland got a goal back late on through substitute Lana Clelland, but the result will be less disappointing than the nature of their performance, as they offered nothing going forward until it was too late, just like in their opening defeat at the hands of England.
As they had done in that match, they found themselves 2-0 down at the interval before a crowd of more than 13,000 at Roazhon Park, including a large contingent from Scotland and FIFA president Gianni Infantino.
A poor headed clearance by captain Rachel Corsie led to Japan taking the lead midway through the first half as Iwabuchi sent a shot high into the net from the edge of the area, over goalkeeper Lee Alexander but underneath the crossbar.
It took a Kim Little goal-line clearance to prevent Japan skipper Saki Kumagai from making it 2-0, but Japan were handed the chance to increase their lead in the 37th minute when Sugasawa felt a slight pull from Corsie in the box and went down.
Sugasawa duly dispatched the penalty, and Hina Sugita then hit the bar from close range.
Scotland did better in the second half, helped by the introduction of Claire Emslie, who had scored their goal against England, and some good saves from Alexander.
However, Erin Cuthbert hit the frame of the goal from close in and their appeals for a penalty for a handball in the box by Risa Shimizu were waved away by the Ethiopian referee.
Clelland, of Fiorentina, did find the net from 25 yards with two minutes to go, but it proved to be a mere consolation, and their hopes of qualifying for the last 16 at their debut World Cup are slim before a final group game against Argentina in Paris.