Define your scope. Everything south of Sub-Saharan Africa?
Theoretically , if , by some dint of several rather nasty PODs , the Europeans nations develop a colonial doctrine similar to Lebensraum , rather than the White Man's burden or Civilizing mission , then this could happen over the course of several decades.
That is , if such an attempt was made over several decades.
It is worth noting though , that the Native Americans and Aborigines had far lower population levels , and inhabited lands far more hospitable to European colonization.
I'd think that the scramble for Africa would need to be limited to two , or perhaps three European nations at most for something as horrific as that to approach plausibility though . If the atrocities of Belgain Congo were replicated on a near continental wide scale , and the nations involved in Colonization were both few , and ruled by absolute monarchs , or at best , Prussian style Constitutional Monarchies , it might be possible , provided that the ones seating on the throne are like Leopold of Belgium ,or worst.
Please bear in mind that both Australia , and much of North America was controlled as one political unit , and that the public outcry over the destruction of native populations there , for various reasons were much more muted than the outcry in Europe over Belgian Congo.
Hence , I propose a few PODs. Note that this likely would result in a rather grim-dark , dystopic world.
Let's say that the Napoleonic Wars eventually die down in the favor of the French , with Europe divided into French , and Russian sphere of influences. I think with enough PODs , it might be within plausibility (though not a very likely scenario) .
The result is a Europe governed largely by semi-autocracies , that develops the hallmarks of what we would recognize as Dictatorships. Let's assume that the Industrial Revolution develops at the same rate in Autocratic Napoleonic Europe (but one where the rule of law and institutions and urbanization is much more advance than Czarist Russia).
Let's assume that it's only slowly liberalizing as Napoleonic Europe begins conquering Africa in a fit for Colonial Glory , starting in the mid 19th Century. The process is extremely brutal , and with a still tightly neutered press and censorship in the motherland , much of it goes undocumented. Belgian Congo writ large breaks out throughout Napoleonic Africa occurs south of the Sahara . Tens of millions are killed , to the general ignorance of the European populace.
Perhaps , during this period , a bloody Muslim revolt , and a Ottoman-Napoleonic France war breaks out. The Ottomans looses , and the Muslim revolt is put down with astounding massacres. Many French , Spanish and Italian settlers in North Africa are massacred at the start of the war. Public opinion consequentially looks the other way , when the Muslim North African population is subjected to numerous massacres . Indeed , public opinion demands revenge. The Emperor complies. Economic pressure, massacres , mass expulsions and force conversion very much reduces the Islamic population in North Africa to a shrinking , persecuted minority. North Africa , is subjugated decisively , but at an appalling human cost.
Perhaps a second war is fought between the British and Napoleonic France in the late 19th Century , over something very similar to the Fashoda Crisis . During this period , there are numerous uprisings in Sub-sahran Africa . Nevertheless , Napoleonic Europe wins after several years of brutal fighting, and puts down the rebellions with great brutality.
Afterwards , Eugenist in Napoleonic Africa captures the ear of the Emperor , and much of his court , and large sections of the senate. With propaganda , and tales of murders of Imperial Citizens ringing in the ears of the general European population , and several business interests in the Empire in support ,the Emperor decides to implement the equivalent of a final solution on the African continent , South of the Sahara, near the turn of the 20th Century .
By 1930 , the process is complete. Nearly 90% of the pre-colonial African population is destroyed , by mass expulsions , deliberately induced famines , de-facto Slavery , Genocide (called Clearances) , concentration camps and more.
By the time a new Emperor seats on the throne , it's too late for the native Sub-sahran Africans. Malaria treatment , antibiotics and medicine has made much of Africa livable . There are large European populations in the Highlands , and South Africa. In the other , less hospitable parts, geologist have made numerous discoveries of valuable minerals , while the European timber industry has begun the first stages of deforesting central Africa.
By the fifties , a second wave of colonists - laborers , technicians , engineers, miners , surveyors in the employ of European mining and logging concerns have swamped previously uninhabitable parts of Africa (from a European perspective). In this second wave , more dispossession occurs to the remnants of the Native Africans. The survivors are crowded into slumps of Great European colonial cities, or working for slave wages at the most menial , dangerous jobs in European owned and operated Gold , metal , Diamond and other precious stone mines.
It's only in the 70's and 80's , as a result of a falling Imperial birth rate for people of European descent, that the proportion of Indigenous Africans as part of the African population south of Sahara begins to climb again , but from an extremely low base of 1-2 %. .
As for North Africa , the population has largely been assimilated. Those that have not been killed , or forced into the Sahara (or flee to the Sahel) have largely become French speaking , and Catholic. Islam in the Magherb is a memory , obliterated during the 19th Century.
To this day , the rest of the Islamic world still distrust the Empire for that. The atrocities of the Maghreb and Sahel are still rallying cries for fanatical Islamic Fundamentalists . Recent terrorist activity in Europe has repeatedly referred to the lost lands of not just Al-andalus , but also the Maghreb.
The Empire is locked in a Five way Cold war between the British Empire , the Americans , Russians , and Chinese. The Council of Nations comprises of the same five members as the UN security council of OTL: France , Britain , USA , Russia and China. The world is significantly less democratic , and human rights less emphasized (if the butterflies haven't warped that concept , or replaced it with another ). Four out of the five are still Monarchies. The fifth is nominally a democracy , but Oligarchical (in this TL , the gilded age never really ended , but simply evolved). These are the five wealthiest and largest nations on Earth. The Great Game is still played today in the hosts of more minor states between each Nation - Iran , parts of South America , a Pan-Arab Hasemite Monarchy , a Greece where the Megali idea has suceeded beyond all expectations (thanks to Russian and French meddling in Ottoman affairs ), Siam , Japan ....
MAD is still in effect , more so in this OTL.
It's not a pleasant TL. But this not a pleasant question.
But it's plausible? Maybe even likely . with enough PODs. You just need Anti-biotics , Quinine , a single , or at most two or three colonizers in Africa , earlier discoveries and exploitation of natural resources in Central-Africa like Diamonds , and oil in Nigeria , etc....
Most of all, you need to retard the development of liberalism , the concept of human rights , civil society , and slow down the gradual diminishment of the powers of Monarchs in Europe , while allowing Industrialization to continue at a perhaps slightly slower pace.
In other words , the OP proposes a scenario that can only mean a more dystopic world than OTL.