Here is my itinerary, followed by my question:
X (a European city) --> New York, JFK New York, JFK --> Y (a South American city)
Do I need to pass through the passport control at JFK if I purchase those two flights separately?
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There are no transit areas in US airports. Pathways through US immigration are the same regardless of whether you are leaving the airport immediately afterwards, taking a domestic connection, or taking an international connection. Thus, you need to have appropriate documentation to enter the US for whatever is your intended purpose (in your case, transit).