Japan struck as early as fifth minute through a penalty corner and added two more goals in the next two minutes to leave India gasping 0-3.
The Indian team earned their first penalty corner in the 14th minute and Rani converted it to reduce the gap.
The game went into half time with Japan leading 3-1.
India came out of half time stronger, and immediately tested the Japanese goal keeper in the beginning of the third quarter, only to be thwarted by their goalkeeper who cleared the ball off the line.
Also Read
Deflection by Poonam missed the target, while captain Deepika also missed a chance in the quarter.
Late in the fourth quarter, India had a flurry of PCs as they looked to convert a goal to put their opponents under pressure. Japan's goal keeper Asano Sakiyo was called into action as she cleared off the line from Rani's try in the final minutes to ensure her team qualified for the next round.
India next play Canada in the classification game on Saturday.