It might depend on the school, but at Berkeley they are different exams. The prelims are taken early on and cover undergraduate physics material, more or less. The qualifying exam is a test related to one's area of research, and is taken later on. UIUC has a similar system, but, interestingly, the names of the exams are reversed. UCSD has an entrance exam, taken at the very beginning, a departmental exam (both of which are general physics tests), and then a qualifying exam related to research.
These are the only schools I know about, but it seems that schools will typically have an exam early on that covers physics in general, and then a later exam related to one's area of research.