I'm currently on day two of a three day course of medication for a UTI. I'm still experiencing back pain along my lower back but there is no more pain during urination. Should I wait until I have finished the antibiotics to see my health practitioner about the pain? In the meantime, is it advisable to take pain medication for my symptoms along with my antibiotics?

You can take pain medication along with the antibiotics. Make sure to take the antibiotics exactly as prescribed. 2 days isn't considerably long to not be experiencing any pain at all. Try a heating pad as well.