It's a matter of style, where emphasis is placed on the particular tree (this is why the repetition "ap autou". Your literal translation could be "lest from that tree, from which alone I commanded you not to eat, from that you ate". This is not that bad, I think, and it keeps the original emphasis.
Notice also how the original places the act of eating at the end of the sentence, where it repeats eating two times. You harry to mention eating, thus transforming a style that implies a most significant action, with the most important consequences, into a simple narration.