Of course we can - and do - vaccinate against bacterial diseases, as these are some of the dangerous infectious diseases. Among these are:
* Tetanus (although here the vaccination is targeted against the toxin, not the bacterium itself)
* Tuberculosis
* Diphtheria
* Pertussis
* Haemophilus influenzae type B
* Cholera
* Typhoid
* Streptococcus pneumoniae
* Meningococcus: against the strains ACWY, B
A list of the vaccines against bacterial diseases can be found here.