Yes, you can. You're actually able to catch two of them, so if you'd like, you can catch a normal one (perhaps as trading leverage), and then KO or run away from the second one to hunt later (it'll reappear in the same area). I've tested this and, while I haven't gotten around to actually hunting it yet, I've seen other people get a shiny Blacephalon after the postgame like this. I don't know for sure whether both will reappear if you KO/run away from both of them, but I honestly don't see why they wouldn't.
