In Philip K. Dick's alternate history novel "The Man in the High Castle", the victorious Nazis are depicted as having completely wiped out the native population of Africa. Was a genocide like the Generalplan Ost in the Nazis' longterm plans for Africa?

In short, no. And even things like the Generalplan Ost are less clear in what they were intended to be than people often assume but more on that below.

The thing about post-war plans is that they tend to be extremely tentative and uncertain until the point the war is actually over and even then they can change in some rather crucial details. Just as a quick look at the Allies: The first sketching of plans began in earnest in 1943 after first territories in North Africa had been liberated and many things weren't actively settled until Yalta and Potsdam in 1945 and even then substantive changes remained, f.ex. Yugoslavia becoming a socialist country. Plans for how the occupation of Germany would be handled concretely weren't finalized by the time the first German city, Aachen, was liberated by the Western Allies. So, post-war plans by the Nazis at any point in time are to be taken with a huge grain of salt and were subject to constant change.

Generalplan Ost is actually the best example of this. I've written about it before here and the crucial point is that the GPO was never fully implemented, only in very small parts. Because of rising, cost, effort, and the course of the war, planning for the GPO stopped and all started projects in connection to the GPO came to a halt after 1942, when the Nazis decided instead to use their available resources and manpower for the war and the Holocaust (which had been a crucial part of the GPO). What was implemented was very piecemeal and compared to the grand vision of the plans, comparatively small scale.

The same holds true for other plans, some of which never really made it out of the planning phase. Here the example of the Madagascar Plan is very fitting. I've written some more about that here and with this example, the gist once again is that the so-called DIII proposal is genocidal in its intentions but only every existed in a very, very rough outline that never made it past a draft phase due to the fact that it wasn't feasible under existing conditions – Allied control of the seas – and that it was never fully endorsed by the entire political establishment of the Third Reich, which due to the political structure of Hitler's Germany had a tendency to be at each other's throat the entire time of its existence.

This last point is important because there only existed one agency charged with developing policy towards Africa: The NSDAP Office of Colonial Policy (Koloniapolitisches Amt der NSDAP – KPA). The KPA had been founded in 1934 and drawn together Nazis who had been involved in colonial policy during the period of Imperial Germany prior to WWI and charged with the mission of developing plans on how to bring former German colonies back under German control. It's head was Franz Ritter von Epp, an old Freikorps member and early Nationalsocialist.

Epp was rewarded this way for his continuing loyalty to the Nazi movement. A former soldier and successful Freikorps leader he might have been but a shrewd political operator he was not. Within the power structure of the Third Reich all his attempts to re-make the KPA as an official state agency rather than a mere party office failed and in 1938 the German Foreign Office won a significant political victory over Epp by taking charge of all efforts to win back the German colonies. Henceforth Epp and the KPA were charged with developing plans for Africa in general.

For the next two years, Epp and his fellow Nazi colonial administrators without a colonial empire sat around and dreamed up megalomaniac plans for how a new German colonial Empire in Africa would look like. Most of these plans however were either so bad or so unfeasible that they apparently never made it to the phase of being written down coherently and therefore there is little record of them whatsoever.

Only in 1940 with Axis success in North Africa did the KPA have its fifteen minutes of fame. What they essentially did was dig up old drafts from WWI Germany for what would happen after a German victory in Africa and slightly re-tooled them. Effectively, they planned for a large central African German colony encompassing the majority of British colonies in the area and containing Tanganjika, half of Nigeria, Uganda, Kenya, Nordrhodesia and the Kongo with South Africa as a German puppet state. attached to it. They drew up racial laws more modeled along Nazi lines for these territories that were closely oriented also on those in South Africa and Rhodesia. Their plan also included some presence by the SS.

However, this plan – and this must be emphasized – was really, really rudimentary and while the KPA did already start preparing future colonial administrators for their role, it lacks the detail that – say – even the GPO had. This is all laid down in a document that doesn't encompass more than a good 30 pages of typewriter script, which isn't all that much.

And Epp's fifteen minutes would be over soon anyways. Going on into 1941 and 1942 losses in North Africa squashed dreams of a Nazi colonial empire and in 1943 the KPA and all Nazi planning for Africa was officially ended by Hitler and Bormann with all resources going into planning for the East.

Epp's plan did include very harsh racial laws that certainly could be seen as a preparatory stage to genocide or in as much as South African and Rhodesian policy edge on forms of cultural and other genocide but it did not include such concrete measures like the GPO, the Hungerplan or the Holocaust. Like so many other things it was a Nazi fever dream fantasized up by people who saw themselves as the future white supremacist overlords over the world and who thought that they could colonize Africa on a 30 page memo.

Edit: There still is an interesting history to write about Nazi war criminals fleeing to Africa though as just a few crumbs of information I dug up for this answer reveal though.

Sources:

Alexandre Kum'a N'Dumbe: Was wollte Hitler in Afrika? NS-Planungen für eine faschistische Neugestaltung Afrikas, 1993.
Sönke Neitzel: „Mittelafrika“. Zum Stellenwert eines Schlagwortes in der deutschen Weltpolitik des Hochimperialismus. In: Wolfgang Elz (Hrsg.): Internationale Beziehungen im 19. und 20. Jahrhundert.