I believe the best answer to this is in the thread, "Was there a theoretical endgame to Apartheid in South Africa from the perspective of White South Africans?", make sure you catch /u/khosikulu's answers down the thread, especially through the one that begins "Not one, but actually ten". There are at least half a dozen comments throughout the thread worth reading.

But the very short summary of the responses was to create a White dominated South Africa, with Black residents not being part of South Africa but being citizens of 10 independent or at least quasi-independent "Bantustans" based on ethnic origin (Zulus in KwaZulu, Xhosa in Ciskei and Transkei, etc). Even if these people lived and worked in major South Africa cities, in the end game, they would be citizens of "their own homeland" (even if they had never been to that homeland) and at best "temporary" workers with limited rights within South Africa. These homelands would be run by the "traditional elites". By the time Apartheid ended, the Bantustans were already partially implemented, with the South African government recognizing several of them as independent. At one time, similar homelands were planned for South West Africa (Namibia). It is unclear what the Nasionale Party had planned for people who weren't White or Black, i.e. the Indians and the Coloureds. By the 1980's, at least, the Apartheid government was slowly moving in the direction of more rights for Indians and Coloureds, for example through the Tricameral Parliament, where each community got to "decide its own affairs" and members of all three communities would decide "general affairs" (though Whites had a big enough bloc of votes that they didn't actually need the other communities to pass measures dealing with general affairs). I have no idea if this was always the end goal for Indians and Coloureds under Apartheid, or a solution developed in the 1970's or 80's, but I'd be curious to know how they fit into the original Apartheid plans.

I'll just ping /u/khosikulu and /u/profrhodes (two of my favorite flairs on here; if anyone wants to learn about southern African politics and history, go to their profiles and sort by "top"), just to see if either happens to have the time or inclination to add anything to that older thread.

Quick edit: I found a bad history post by /u/khosikulu post that also delves into similar issues and is likely of interest (I should note that post conforms to the norms of /r/badhistory so its tone is slightly different from a typical /r/askhistorians post). This sentence might be a particularly good summary:

Apartheid had two faces: one that claimed equality with separation in theory, and one that facilitated subordination and subjugation in fact.

In theory, Blacks were to be citizens of Bantustan only and there would be "separate development" along racial lines, but in reality the South Africa economy and society heavily depended on cheap Black labor, which meant that Blacks alongside Whites within the Apartheid state was inevitable. The Bantustan system was just meant to assure the White minority that Black could only make political demands in the noniminally separate Bantustans, and that the South African government would be minimally if at all accountable to them.

Edit 2: since you specifically mention Israel as a potential "apartheid state" in your header, I'll just link to a discussion I had in a different subreddit about the comparison (in a response to an article that makes the opposite argument that I do, in case you want to read it as a point/counter-point thing).

Quick response to a comment that has since been deleted, because it's important to correct a misconception that, in the end, became sort of true:

These bantustans only consisted of about 20% of all of South Africa, and wasn't fertile at all.

One quick correction here, because I work on land and that involves the fraught policies of betterment and rehabilitation: the 8%, then 13%, and finally closer to 18% of South Africa that was set aside for Bantustans (not counting the High Commission territories that white nationalists like to pretend "count") was in fact some of the most fertile land in the country. Those were the areas where kingdoms were able to sustain and resist settler displacement for extended periods of time, managing great herds and large populations, so they had access to water and good soil. Of course, this is something apartheid apologists do point out as well.

What they miss is the effect of confining a majority of the population (even discounting the migrants) into these areas. The land was exhausted after only a few decades, people couldn't shift cultivation or grazing during drought years because they were fixed in location, and in most cases they were actually barred from accumulating commercial amounts of land. It was a system that presumed "subsistence agriculture," and at the same time, communities recognized that people wanted if at all possible to avoid working for mines or white farmers as migrants and so tried to make room for them to cultivate some sort of land. All of that meant environmental crisis by the late 1930s.

Enter the Natives Trust and Land Act of 1936, and particularly the Trust itself (that's how the land went from 8% to 13%, by the way). They brought in scientists to try to determine how to manage the land because clearly black farmers couldn't do it, in one of the most obviously self-fulfilling prophecies I have ever seen. They prescribed radical reconfiguration of occupation patterns to put dwellings atop hills and cultivation below, cull herds forcibly (which is a horrific thing because that's your social wealth too), and generally force people into even more marginal existences by pushing them off lands they knew into subdivided plots they didn't. A good, complete history of betterment and rehabilitation policies is still to come, but bits and pieces exist in any rural history of SA during the 1940s and 1950s. (William Beinart's book on conservation and livestock has some information; Bundy and Beinart have a few chapters together as well, in Hidden Struggles in Rural South Africa.)

So you will sometimes hear (white) people bristle at the suggestion that the Bantustans sat atop unfertile land, but the reality is that it was made infertile by those policies. Heavily overused factory-farm land in the Free State (for example) also began to erode, but white farmers enjoyed massive subsidies for engineering works, while in the Transkei and Ciskei they got rocks for contour breaks and very rarely could they fill the sandy dongas that cracked the land open and eroded it from below. Jim McCann and Kate Showers, among others, talk about some of this relative to Lesotho vs. the Free State; Lesotho had many of the same problems, and still is a water/labor reservoir for South Africa.

Follow-up on another aspect of the analogy: were there any "anti-Apartheid" activists in South Africa who promoted complete independence for the Bantustans, rather than integration and democracy?