The watch which I bought from Japan is a birthday present for my sister.
Does the sentence need some commas?
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If you really mean that as a nonrestrictive clause, then I'd use two commas -- surround "which I bought from Japan" with commas.
However, if I were editing this sentence, I'd use "that" instead of "which." It really depends on the intention of the sentence.
If the sentence is answering the (perhaps unstated) question "What are you going to do with the watch from Japan?" then I'd say "The watch that I bought in Japan (or brought from Japan) is a birthday present for my sister."
If the question is "What are you going to do with that watch" and the fact that it was brought from Japan (or bought in Japan) is extra, "by the way" information, then you could use: "The watch, which I bought in Japan" (or brought from Japan), is a birthday present for my sister."
By the way (and I know you didn't ask, so forgive me), "bought from Japan" sounds odd, as if it were purchased from the Japanese government or something. I'd use "bought in Japan" or "brought from Japan."
I hope this helps!