You can read in Mandukya Upanishad that, "All this is verily Brahman, and this Atman is Brahman." Thus, it's not that they are two. Even Vedic Hinduism says that realizing (where) the nature of self (comes from), is realizing that it is what we call Brahman itself. The separation is illusory -- it seems that consciousness is within and separate (Atman), but, upon closer inspection, realizing its nature, it becomes clear that it is the whole world that is "within" consciousness. Consciousness, which, nonetheless, still "looks" from within.

Since conceptualizing and naming something creates the illusions of a separate thing, Buddhism is merely more particular in not naming "the absolute" and saying that Atman is illusory (which it is, even according to Hinduism). And yet, even Buddhism calls the Tao that cannot be named "emptiness." And ironically, Buddhists are obsessed with finding Emptiness where there is no self. To the point that they deny that emptiness is also form (even while form is, indeed, empty) and that that is their "Buddha nature," aka Brahman.

I'd say that the same problem had to be widespread in Hinduism in Siddhartha's time (as is until today) and he, according to legend, set out to remedy that (IIRC, he complained that all his teachers mistook meditative absorption for abiding liberation of nirvana). Be as it may, today, it plagues Buddhism too.