You don't, Confluence permissions are permissive - you allow people do stuff in spaces, not set flags to stop them in general.
There's also the layer of page restrictions over the top of that, but they're done by page (and cascade to child pages), not at a top level.
You will need to remove whatever is granting your users general access, re-adding the ones that are needed, and then leaving the spaces you want hidden off the general list of accesses.
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