how to avoid to being blamed of self-plagiarism in this case?
There are two issues here. One is self plagiarism as the term is commonly used and there is what a University will accept for any course or degree work. The latter can be stricter than the usual rules because the goals are more nuanced, involving the student's education, not just the validity of the work. 

I doubt that this can be considered self plagiarism, provided that what was submitted to both places is the same. Keep in mind that the purpose of self plagiarism is that a reader needs to be able to see the entire context of a work in order to judge it and to extend it. If people just copy without citation from their own work it breaks the chain of reference that scholars require. But publishing the same work in different venues doesn't do that. Each work is complete. And when copying does occur, citation avoids any claim of self plagiarism, since the thread of context is maintained. 

But, given that, the student may still not be meeting university requirements, in particular if there is a rule that submitted work not be previously published. If this is the real nature of the problem, then you need to find a local solution, since we can't advise on rules we haven't seen and have no ability to enforce or not. 



Multiple publication of the same work might run afoul of copyright rules, but I don't see a hint of that in this case. And multiple publication does occur as when old papers are put into collections. This can be valid or not. But it isn't plagiarism or self plagiarism.