It is actually correct - but very archaic and, unless the context is archaic or poetic, it sounds weird. As Mark said, "He knew not what he was waiting for" is better, but still slightly archaic - you would usually say "didn't know" instead of "knew not". But, again, if you need something old, or something that sounds like poetry, "He awaited he knew not what" is fine.

The word order is rather strange. It would make more sense to say, "He knew not what he was waiting for," but it also depends on context.