Johannesburg, South Africa tickets are priced $532 to $570 from Newark EWR or New York JFK with Lufthansa and Swiss Airlines via Germany or Switzerland. These tickets are also sold through United Airlines.
The catch is low fares require all day layovers in Frankfurt or Zurich on most flight itineraries I checked. An all-day layover can be an opportunity for sightseeing or sleep between long haul flights. Both airports have good transportation between airports and city.
Play around with dates and there might be two dates with more reasonable layover times in each direction.
Lufthansa Airlines ticket for Swiss and United flights
Newark EWR – Zurich ZRH – Johannesburg JNB – Zurich ZRH – Newark EWR
Lufthansa Airlines New York JFK – Frankfurt FRA – Johannesburg JNB – FRA – JFK