I understand the equivalent expression in Japanese is:
I wonder where you found that because by far the most-often used Japanese translation for "Whatever will be will be." would be:
「なるようになる」 or 「なるようになるだろう」
These phrases do not use a counterpart of "whatever" in them as they already sound completely natural without it to us native Japanese-speakers.
But if you insist that a word for "whatever" be used, one could say:
Also common would be:
We love using our 「しか～～ない」 construct.
(I will not even explain the ungrammaticality of the phrase "Que sera sera." That is only American-made Spanish or French, which is just like the weird Engrish used in Japan.)