What is the difference between God’s omnipresence and pantheism?

Pantheism, from the Greek "pan" for "everything", holds that God is everywhere and in everything in terms of His nature and being. In pantheism, God is everything and everything is God. In pantheism there is no personal God.

God's omnipresence, biblically speaking, is not pantheism. God alone is eternal in the absolute sense. God existed before the existence of matter. Some scholars of secular science proclaim the eternal existence of matter. Not every scientist in secular science agrees. Biblical scholarship agrees with those secular scientists who believe that matter is not eternal. Matter has a beginning. That beginning, biblically speaking, is God. Only God is eternal in an absolute sense. God is the Creator and He creates matter. He is not in this matter, but this matter comes from Him as creation ex nihilo. Although God penetrates matter and is in matter in this sense, He is not matter itself and matter itself is not God. Matter comes only from God and is the result of His act of creation. God Himself is Spirit. Spirit is non-material in its essence. So matter emanates from God, but once emanated it is not God but the creation of God.

Living beings are an act of creation, either directly or indirectly. Directly at the beginning of creation for the first races, from which, through evolution, other kinds of animals emerged. God is not those animals. He is the Creator of those animals and plants. Plants are living beings, nephesh on a lower level than animals. God pervades all parts of plants and animals, and their life as individuals is due to the activity of God's life-giving Spirit. But neither plants nor animals are God. God penetrates them, animates them and gives them life, but He is not the plant or the animal.

The same is true of man. God created man and therefore man receives his life from God. God gives life to man. This is true of every individual. As long as God gives life to the individual, the individual has life. Man is created in the image of God. This does not mean that man is God himself, but that he is like God, not in the physical sense, for God is spirit. But man is created to reflect God's character, God's being in the moral sense. This is true of both man and woman. God is neither man nor woman, God is Spirit. Man and woman are both part of the reflection of God according to creation. Together, man and woman reflect the whole picture of the image of God that God intended for human beings. Moreover, the relationship of unity between man and woman in the moral and ethical sense is a reflection of God's being. Lack of unity and unresolved conflicts therefore diminish, limit and contradict God's plan for human beings as individuals and as a reflection of God.

God gives life and is present in this life-giving activity in every human being, but God is relationally present in the human being only when the human being desires and consents to this. Otherwise there is no relational presence of God in the person. God nevertheless has control over the life of each individual, whether in relationship with God or not, and can speak to each individual, but the individual's choice determines the way in which God relates to that individual and the extent and manner in which God speaks to that individual.