This is a very good question.
Let me start by saying there are 2 kinds of relative clauses: defining and non-defining.
If you put a comma before "who," it will mean that you are giving extra information about your sister. In this case the relative clause (who (had) just got back from Japan) doesn't define or classify the noun (sister), the main clause still makes sense without it (I received a gift from my sister - and everyone understands who exactly, perhaps, because you have one sister).
If you decide not to put a comma before "who," it means there is a need to define the sister - which sister exactly gave me the gift? (it may be important if you have more than one sister)
Thus, a defining relative clause identifies or classifies a noun/pronoun in the main clause. It gives information which is necessary for the sense of the sentence.
Here are a few more examples:
The members of the team, who had sponsors, flew to the championships in Ottawa. (All the members of the team flew to Ottawa.)
The students who passed the test received a prize. (Some of the students didn't receive a prize.)
Source: "MyGrammarLab Advanced" by M.Foley and D.Hall
For more information on relative clauses, check out this blog.