If Home Affairs were smart, they'd be modelling this based on what Australia and New Zealand are doing.
Neither country issues physical passport labels any longer (NZ will, on request, but only after your visa has been approved, and you will need to fork up an extra $130
and courier your passport to Auckland). Instead, one is issued with a confirmation letter showing the details of the visa one holds (which is an electronic record in the immigration database), which one then prints out and presents at check-in and border control. INZ has a handy explanation of their eVisas
here (together with sample letters).
That said, both countries often require some physical passport evidence. NZ requires South African passport holders to submit their passports for physical verification if it's a passport they don't have record of: for on-shore South Africans, this requires couriering or physically dropping off the passport at the Visa Application Centre in Pretoria (but they return it as soon as it's verified and scanned in, usually a day later). Australia requires the applicant present oneself in person with passport for both passport verification and biometrics capture.
The eGates work with biometric passports only (so Home Affairs should be looking at issuing those, if they aren't already), and only citizens and other trusted countries (usually visa waiver countries) get to use them (so, as other posters pointed out, expect South African passport holders abroad to still have to go through manual processing). I don't have first-hand knowledge of these things, but as the holder of a British passport (and with her NZ Resident Visa linked to that passport), Mrs Kel does, and goes straight off to retrieve our luggage while I languish in the manual processing queue (though, as the holder of a Resident Visa myself, I legally cannot be denied entry permission, and so once I eventually get to the head of the queue, it's 15 seconds processing and done). From what she's told me, the system scans your passport and the biometric chip, asks you some questions about yourself and your intended purpose (depending on what passport you have and if you already have a visa or are from a visa waiver country and are applying for a Visitor Visa on entry), then takes a photo of you and compares this with the digital photo from the biometrics chip. If the system is happy, in you come; if not, it refers you to manual processing.
Note that minors can't use eGates: children's appearances change quickly enough that the eGates are unable to do biometric matching. Hence, I'm usually lumped with families travelling together in the manual processing queue.
Unfortunately, I have little faith that Home Affairs is smart, and every expectation that South Africa will get a flaky, insecure, and tenderpreneured version of both eVisas and eGates instead.
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