When I search Google, "where did you get the black eye?" is almost as common as "how did you get the black eye?"
Is the question with "where" natural to you? And if yes, why?
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It seems reasonable. Asking "where" is implicitly asking not only for the location, but the situation.
There is, perhaps, a little irony in the question too. If someone has a new haircut you might ask "Where did you get the haircut", ie. "which shop". So this is might be ironically treating the black eye as if it was a fashion.
"How" is the obvious question, but "where" doesn't seem strange, and, as you say, google provides plenty of examples.