The separation of church and state affects governance by ensuring that religious institutions do not wield direct influence over government affairs and vice versa. This principle, rooted in the First Amendment of the U.S. Constitution, promotes religious freedom and prevents discrimination based on belief systems. It fosters a pluralistic society that allows diverse faiths to coexist without favoring any particular religion in public policy. The separation is crucial for maintaining a secular state, which helps to uphold democratic principles and safeguards individual rights.