In one of my works I cite several times this kind of publications, but I don't know the recommended procedure to refer to them at the end. For articles I usually take bibtex code from Google Scholar or a similar site, but these papers do not figure there. I'm not sure even whether the best writing practice is to cite them or just to cite the main article, when referring to some specific information that is not published in this main article.
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Supplementary information is always part of a paper. Just cite that paper as you would normally do. If you want to specifically mention in your text that you are referring to supplementary information you can just call it by its title, something like "(Supplementary Figure 2)".
