I always have problem deciding which one to use.
After understanding that, the darkness finally [...] from my eyes.
Should I use cleared from, cleared up from, or cleared away from?
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I would say you can use either cleared from or cleared away from here.
They are fairly interchangeable.
That said, some might argue that cleared from implies that the darkness dissolved on its own into nothing. And, cleared away from implies that the darkness moved away from your eyes, but is still present in the universe somewhere. (I suggest looking between your couch cushions.)
Cleared up from means a condition improved (e.g. your acne cleared up).
I will source/disclaim all of these answers as being per my ear as a native speaker of American English.
If we look up the meaning of clear in Google dictionary it says: brighten (up), lighten, clear up, become bright/brighter, become light/lighter, become sunny. Therefore, as a verb it is more than suitable to use in concomitance with the noun, darkness. Nevertheless, as Susan mentioned in the comments, "darkness lifted" is by far the most familiar expression, so one is left with the dilemma of choosing a well-known expression for one much less so. Only the author can make this final decision.
Onto some statistics: "Cleared from" in Google books achieved only 371 results.
Presently the darkness cleared from his mind and he opened his eyes
To clear away means to remove from sight, as in to clear the table away.
Google books yielded a respectable 3,440 results for "darkness cleared away".
As the darkness cleared away, Selena was able to focus and identify the appearance of a small child
To clear up, a phrasal verb which is often used when something untidy or messy needs clearing. It can also mean to clarify, explain or resolve a mystery, an enigma, or a misunderstanding. The weather cleared up, means that it was cloudy and possibly it was going to rain but now the sky is clear.
Google books yielded, astonishingly, a mere 34 results.
When the long darkness cleared up he found himself lying on a cot in a strange room.
If I were asked which one to choose, I would opt for "cleared (from). The resulting phrase sounds natural and I would have no difficulty in understanding the author's intent.
After understanding that, the darkness finally cleared from my eyes.