The scientific method requires evidence. This evidence may be deductive, inductive, or direct. Much of what is science today has been deduced or inferred by observing nature and understanding the ways it works with experimentation.
These methods leave us with two aspects of nature — that which we understand and that which we do not. Science merely refuses to label the latter as god. It is really not that complicated.
It should be noted however, that there is no universal consensus on what “God” even means. Some people understand it to be the Biblical father figure mentioned in the Christian Old Testament. Some consider it to be the god mentioned in the Islamic holy book. We Hindus have our own pantheon of gods.
In order for science to accept that god exists, there has to be some kind of shape to the idea of god. Science deals with the tangible and when it comes to logically explaining the way human beings have used imagination to make sense of their world, the only tangible thing science can find is the ways this quest has affected politics, war, and human civilization. These do not represent the god concept at its best. In addition, the sublime aspect of god — that which exists in the minds of believers — makes sense to science only as functions of the human brain powered by evolution by natural selection.
In summary, science has not proven that God does not exist, but that is because it does not have to. As far as science is concerned, anything that is offered without evidence, can be dismissed without evidence. And lack of evidence is a good reason to not believe.