If you arrive into SA and leave the airport (e.g. the transit area of JNB or CPT) to drive from SA to anywhere else, you're entering South Africa. You're not "transiting" SA.
It's not a 90 day tourist visa.
If you are traveling to SA for 90 days or less you do not require a visa.
https://travel.state.gov/content/tra...uthAfrica.html
https://www.southafrica-usa.net/home...sitorsvisa.htm
In my experience of 20+ years of flying into SA, immigration/border officers (at JNB) sometimes only cut you 30 days on entry (I've found it can sometimes correlated to the date of your return ticket). I've found this to be completely arbitrary and random by JNB border control. But, I've never had the need to fight it. On several occasions, I've come in to SA - stayed for a time (less than 90 days or whatever time allotted by the officer), left to go somewhere else (either my origination point or somewhere else), then come back to SA and presented myself again and have NOT been hassled about coming back in for "another" 90 time period. But your mileage may vary ... wildly.
Also, it's not been important to me but keep in mind SA has been opening and closing land borders quite a bit due to COVID. I don't follow it b/c I haven't had to deal with it (I'm concerned about entry by air).