First, sorry to hear this happened to you.
Most important question: did the letter or documents sent back to you give any guidance on what you should provide, i.e. anything more specific than what you had done? Obviously if that tells you what you should provide, do that.
But since you're asking, I presume it did not.
Now background: it seems that in many countries notaries public will NOT sign or witness documents that are not in the national language. (I experienced this for Russia, not Brazil).
I actually approached in a similar way to how you did this: translated (certified translation) into Russian, signed and witnessed by the parent, then certified translation back into English. I provided a letter of explanation - short - explaining why I had to do it this way. And it was accepted by IRCC for processing and not returned (application still in process, so it's possible we will be asked to provide something more in future). I don't know why this approach was accepted by IRCC and yours was not, i.e. if there is some detail of Russian law or IRCC procedures that made this acceptable, or that the translations were all certified, or what exactly. It is possible - perhaps not likely but possible - that the IRCC approach was a mistake by someone who did not know that this is the 'normal' way to proceed for Brazil.
Parallel to this I had inquiries to IRCC and the Embassy to see how I should proceed - unsuccessful (no-one was able to find). So I proceeded as above. After I had submitted, I found a version of the IMM5406 that was in both languages (English and Russian) on one page. It was too late for me to use this form (and I'm not sure it was up to date) - note it was on official IRCC website. The form was included in the country-specific instruction manual for Russia - although as noted this may have been out of date.
The similar guide or website for Brazil (Sao Paulo) does not seem to provide more detail on how to do the IMM5604:
https://www.canada.ca/content/dam/ircc/migration/ircc/english/pdf/kits/guides/e33134.pdf
So the only suggestions I can make:
-inquire direct to IRCC or the Canadian Embassy visa section on how to do this for Brazil (this may be slow or difficult, I just don't know - as I said I didn't have much luck with this approach either);
-contact your MPs office to see if they can help answer this specific question (all they would be doing is contacting IRCC but may have more luck 'shaking the tree' for the correct answer) - note that if the IRCC response was in error, the MPs office may also be able to help clarify and hopefully avoid having a re-submission returned;
-check Portuguese language immigration forums as it is highly likely that others have encountered this particular issue before;
-contact or inquire of immigration consultants on this specific issue - it may cost money, and they may want to do your whole application (for significant extra cost), but perhaps would consider a one-off consultation;
-you could re-submit with the same documentation, double-checking that every step is certified translation and include a letter of explanation;
-have some version of IMM5406 prepared in a dual-language version (certified translations) and have that witnessed and executed.
Sorry these are only suggestions on how to track down the issue and not hard answers, but hope it helps. I am guessing that Portuguese-language immigration forums may be the fastest way to get specific and concrete answers, but only a guess. Also likely that Portuguese speaking consultants (of which many in Toronto for example) would know as well.
And side note, as far as I'm concerned this is a major oversight or gap in the country-specific instructions as the English language form is quite specific about requiring it be witnessed by a notary public, and it seems not that uncommon that notaries will not witness foreign-language document execution. (The existence of a dual-language English/Russian form - even if not current - also indicates that IRCC is at least aware this is not possible in some countries, too). But knowing this is a gap doesn't help you in the here and now.
Good luck.
