The two essential stops
The Apartheid Museum is the clearest, most affecting introduction to the system and its end. Give it a half-day. The entrance tickets randomly assign "white" and "non-white" so you enter through different doors, a small, effective device that sets the tone. The chronological exhibits walk you from apartheid's roots in colonial segregation through its mechanics and its 1994 end. Don't rush it.
Constitution Hill is the former prison, Mandela and Gandhi among its inmates, turned into the seat of the Constitutional Court. You walk the old cells and then stand in a working courthouse that was built to break what the cells stood for. It's the best single site for understanding South Africa's "never again" framework.
Add Soweto
A guided Soweto tour: Vilakazi Street (the only street to have housed two Nobel laureates, Mandela and Tutu), the Hector Pieterson memorial, and a shebeen lunch. Do it with a local guide, not from a bus window. Soweto is a city of millions; a half-day with someone who lives there is worth more than a full day of drive-bys.
How to do it
Stay in Johannesburg for two nights, base in Rosebank or Melville, and give the apartheid-era history one full, focused day. It's heavy. It's also the context that makes everything else in the country make sense. Don't squeeze it between the airport and Kruger.
The order that works
Start with the Apartheid Museum in the morning, when you're fresh, because it's the one that does the heavy lifting. Constitution Hill after lunch, because it's shorter and it resolves the morning with hope rather than weight. Soweto on the second day, or on the afternoon of the same day if you have the stamina. The museums are closed on Mondays and Sundays respectively; check before you build the day.
Why people skip it, and why they shouldn't
Most visitors treat Johannesburg as a transit hub, fly in, connect to Kruger, fly out. The ones who build in one night and a museum day come back changed. The history here is the frame that turns the rest of the country from scenery into a place you understand. It's the single thing most visitors say they wish they'd done more of.