Vaccines save lives. I'm not here to argue about that, take it somewhere else. If you don't agree, for the purposes of this question just imagine I'm talking about some medicine that accomplishes vaccination, but is magically safe from whatever invented danger that bothers you about it.
Vaccines save lives. However, they are not administered to treat a current illness -- they are given to prevent dangerous illnesses from coming.
Since we know that one may only violate Shabbos for a חולה שיש בו סכנה (patient who is in danger for his life) for things that have to do with saving that patient's life (see Rambam, Hilchot Shabbos 2 (English), Shulchan Aruch, Orach Chaim 328), if we would have to be מחלל שבת in order to administer vaccines1, would we be allowed to violate Shabbos to administer vaccines?
1 It's debatable whether any injections are Biblical Shabbos transgressions, see שמירת שבת כהלכתה ch 32:58, and footnote 151 there; it appears that all agree that subcutaneous and intramuscular injections are not biblically prohibited. For the purposes of this discussion, let's assume that there is some universally agreed-upon Biblical transgression involved, such as driving a car in order to get it, or writing a prescription for it.
Answer
Shemiras Shabbas K'hilchasa 32:62 -- one is allowed to inject vaccines where there is a concern that the patient will become dangerously sick.
If a doctor feels that this is urgent, then even biblical transgressions such as driving a car or writing a script are allowed, where necessary.
In footnote 160, there, Rav Neuwirth cites what he wrote earlier, in footnote 60. There, he retells the story about Rabbi Yisrael Salant, who decided that one year (according to Wikipedia, 1848), nobody should fast on Yom Kippur, due to a concern for a cholera epidemic. However, Rav Neuwirth notes there (60) that one should try to do what needs to be done in a different way than usual (שינוי), where possible.
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