Vaccinations are able to provide protection against certain microorganisms because

Vaccinations are able to provide protection against certain microorganisms by creating a memory response. You use memory T and B cells when attacking pathogens and viruses. Basically, your body attacks the dead pathogens in the vaccines. This is what causes you to feel tired, lethargic, and a bit ill after taking vaccines. But in the long run, should you get the flu or be exposed to the virus, your body will remember the strain and attack it more efficiently. So you are not immune to the flu, but you are going to suffer less and heal quicker.