Lufthansa has a relatively low fare at $910 round trip for San Francisco to Johannesburg, South Africa. You can get this fare flying United or Lufthansa to Europe and then South African Airways to Johannesburg in economy class with some good flight schedules of four hours between long-haul flights.
Fares drop to under $1,000 round trip for San Francisco departures beginning in late October through first week of December, rise substantially and drop to low $900s again in second week of January 2016.
Virgin Atlantic and Delta/Air France/KLM also have fares in the $900s round trip. Oneworld with American and British Airways are priced higher in the $1,100 range. A check of my files shows British Airways offered SFO-JNB on June 24 for $961 for November 2015 travel.
Appears November is the low season travel month for South Africa based on my fare searches this year.
Lufthansa/South Africa Airways
$923.15 round trip San Francisco to Johannesburg
This itinerary has an all-day layover in Frankfurt. That makes a good break to catch a train and walk around Frankfurt for the day before the next long-haul flight. Or nap at a hotel or relax/work in the airport lounge before the next long-haul flight.
There are plenty of options for shorter transit layovers in Europe with different Star Alliance routings.
SFO-FRA-JNB-FRA-SFO is a high miles routing at 22,157 miles. The great distance flown is why I would choose a long transit stop in Frankfurt with time to walk around or sleep horizontally in a bed for several hours before jumping on the next long-haul flight.
Need help with low fare searches? Loyalty Traveler Google Flights Tutorials are free articles I have written on how I use Google Flights to find low fares.