It dealt with science masquerading as religion which was totalitarian and the rebels used witches and the occult to defy them and fight for freedom. The "Great God" scientifically produced miracles.

I read this book years ago.

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    Right now, this is a very sparse question. Can you go to scifi.stackexchange.com/tags/story-identification/info and see if you can conjure up more info from the prompts? For example, was it in English? Hardback or paperback? Medieval or modern? Was there actual magic as well? Do you remember anything about the cover? Around what time period did you read it? Are there any books you've already ruled out, and why? – FuzzyBoots Feb 10 at 19:15

Gather, Darkness! (1943) by Fritz Leiber perhaps? First serialized in Astounding Science-Fiction, May to July 1943, and availalble online on the Internet Archive (part 1, part 2, part 3).

This review on Goodreads mentions the Great God and the witches:

Three hundred years after a nuclear holocaust, humanity is ruled by a secretive religious brotherhood, the Hierarchy of the Great God, which uses science as the supernatural means of ensuring its control over an impoverished, predominantly illiterate population. Opposing this brotherhood is a secret society of witches, the followers of Sathanas, seeking to use science to overthrow the brotherhood's tyrannical theocracy. A young Hierarchy priest, Brother Armon Jarles, skeptical of his beliefs and the Hierarchy's orthodoxy, soon finds himself caught in the bitter struggle between both groups. A struggle that is meant to gather darkness against the Hierarchy's grip on power.

Another review mentions the "Great God" producing miracles:

Written in the 1940's this novel postulates a future where the Hierarchy control the populace by using religion as a control. Using science to produce false "miracles" the Hierarchy brainwashes the populace into obedience--the more clever of the 'commoners' are encouraged to join the priesthood.

So, when an group of revolutionaries begins to overthrow the tyrants, the rebels disguise themselves as "witches" and use their science to create miraculous effects ascribed to "Sathanas".

Found with the Google query book science religion "great god" "rebels" site:goodreads.com which returned the Goodreads page, highlighting the second review.

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    To my own embarrassment, I suddenly realize I've never actually read Gather, Darkness, although I've read most of Leiber's other SF/Fantasy material at one time or another . . . I'm not going to correct the deficiency right this minute, but it's nice to have those Internet Archive links available for when I find the time! – Lorendiac Feb 10 at 23:55
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    I seem to remember that "Gather, Darkness" and Heinlein's "If This Goes On" were different treatments of an idea that John W. Campbell suggested. – user888379 Feb 11 at 1:33
  • @user888379 - interesting! I myself was going to suggest If This Goes On even though it wasn't an exact match. – davidbak Feb 11 at 6:40
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    I was going to suggest Sixth Column by Heinlein, but since that one too was based on a Campbell story, I'm not sure I should bother. – Mr Lister Feb 11 at 9:42
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    @MrLister: "Sixth Column" is sort of the inverse. America has been conquered (by people with technology,) and rebels use science disguised as religion to fight back. – JRE Feb 11 at 11:53

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