The principle of separation of church and state manifests in governance by ensuring that religious institutions do not directly influence government policy and vice versa. This creates a framework where laws and policies are made based on secular principles rather than religious doctrines. In practice, it often involves maintaining a neutral stance on religious issues in public education and ensuring that governmental decisions respect the diverse beliefs of citizens. This separation is crucial for fostering religious freedom and protecting minority belief systems, thus promoting a pluralistic society.