This is the official notice I was able to find:
http://www.immi-moj.go.jp/re-ed/EDcard_leaf_en.pdf

Basically that piece of paper (embarkation card) is no longer required nor present in the new form (unless you are a alien resident of Japan, which then you still need that piece of paper, but that's a different form), so that's why the immigration officer didn't staple it to your passport.

I guess with everything electronically stored, there is not need as once they swipe your passport they can retrieve all your entry records, except the part where you answer the questions (for legal reason) that are not part of your passport.