The Welsh youngsters served up a high tempo display of running rugby for 80 minutes as they vied to impress coach Phil Davies ahead of Junior World Championship selection.
The Wales XV turned around 19-3 up at half time with tries from Nick Reynolds, Jamie Davies and Ashley Beck with two Matthew Jarvis conversions to a penalty for Japan.
Early in the second half, Japan hit back with a try from replacement Minamihashi converted by full back Takeshita.
it was then the turn of Wales to score as replacement scrum half Garetb Davies crossed for two tries, both converted by Jarvis to take the score to 33-10.
When play restarted, Japan hit the game at pace and Yamashita crossed for a try at the posts to give Miwatani an easy conversion.
However Wales were not finished and lock Dan Partridge crossed for a try to send the crowd home happy.
