Wales fielded one of their biggest centre pairings, James at 6ft 4in (1.90m) and 16st 3lbs (103kg), and Max Llewellyn at 6ft 6in (1.96m) and 16st 12lbs (107kg). The pair had not started together at Test level before. Tandy named his sixth different centre combination in his 13th international. Wales and Japan have met often of late. This was their fourth meeting in 16 months.
James had two early bursts down the left, but a knock-on — a fifth handling error in 15 minutes — showed the inaccuracy of the opening quarter.
If the tables stay as they are, the sides will meet again for the fifth-placed finish in south-west London.
The result kept the home side in the tournament, but it was a laboured win rather than a statement of control.
Allianz Stadium in Twickenham will host a three-day finals weekend at the end of November.
Those faults let Japan stay in the game long after Wales should have pulled clear.
The display left clear problems: six line-outs lost, worrying indiscipline, and attacking chances wasted by handling errors.