What effect does a good research paper have on a university's reputation and worldwide ranking?
None. One good paper makes its author(s) look good, but does not make the university more or less remarkable (either in term of perception by the research community or rankings). It takes a lot of good output (papers, conferences, etc.) for people to start saying “hey, that university has great research done in so many research groups, it looks like a great place”, and for whatever rankings to be affected.

Unless by “good” you mean “outstanding”, not in the academic sense “quite okay but I’m writing in hyperbolic style” but in the meaning of “exceptionally good; clearly noticeable”. One groundbreaking (Nobel level, if you wish) discovery made at a single institution will help it.