You need to buy the yen from the Microsoft store. Same company, different store.
Edit:
First, I'd say keep your xbox off (not in hybernation, totally off) prior to making the purchase. I have a suspicion.
Select one of those and add it to your cart. Then do the second one. It'll remember you by the cookies. If you're using chrome, it will translate some of the page for you. Then you can proceed to checkout. It will ask you to sign in or do so offline. I signed in using my MS account. Apparently it's global. If you sign in using your MS account, you should see the screen that Dr.Teflon posted. When you select paypal at the top, you will sign into your paypal account to complete the purchase. After I completed the purchase, then I went to a confirmation page with the codes.
Keeping that tab open, open a new tab and go to xbox.com, sign in, and switch the region to Japan. From there, you can choose to redeem a code. Copy and paste both codes and it will tell you your balance in yen. After that search for Dark Souls 3 (You can use english) and it will take you to a page with the game. Select the game and you should be able to buy it using your balance. You should get a confirmation of the purchase. Now switch your region back to your home country/region and close out.
Turn on your xbox. For me, it started downloading immediately.
Enjoy.