Yes, as the father and natural guardian of your child under Israeli law, you certainly can bring legal action to get your child innoculated, according to the recommended programme, as it is your parental right and duty to act in the minor's best interests,and for his/her good.
Issues of health still remain the responsibility of both the child's parents, as functions of their guardianship, even after they separate or divorce, and even if only one of them, in your case, your ex-wife, has custody. Decisions of a child's health are supposed to be made jointly, by mutual consent, and if this is not possible, you, as the child's father can bring legal action, against the child's mother,and ask the court to intervene and rule on the dispute. You can specifically request an order that will oblige her to get the child innoculated. The court may appoint an expert to give an opinion on the matter to see whether, in your child's circumstances,it is in his/her medical interests to be innoculated, before making a decision.
Such legal action can be taken before the family court, unless there is any reason for approaching a religious court (e.g. if the parents are religiously observant). Jurisdiction over matters concerning a child's guardianship usually lies with the family court, even after divorce,unless there is a specific mention of continuing, exclusive jurisdiction of a religious court, in the divorce agreement, once the marriage ends. Outside of this situation, if one parent brings the dispute before a religious court, after the divorce, and there is no exclusive continuing jurisdiction, the other parent would need to consent to the matter being dealt by it, rather than by a family court , for it to gain jurisdiciton.