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Just a little correction - there are actually two places where you can go through security/passport control. This applies to the main one which you are likely to use - everyone who uses the check-in counters uses this one. The second one is thought for transit passengers who already have their onward boarding passes. If you use that one you turn left straight after passport control and take the escalator up the floor level for the CH.

The second one is usually much less crowded and I also use it when checking in (again) at JNB. You just backtrack towards the domestic terminals before you leave the international side you look for the international transit signs.