For a wide variety of reasons, Africa would not have been vulnerable to that sort of disaster, but I'll think of the question as more like: "What if most of the people in subsaharan Africa disappeared"
Well, the first thing that comes to mind, is the sudden death of the slave trade, and the trades dependent on it.
Considering the time period, you have to wonder if this would result in less brutal treatment of slaves, by necessity. Certainly, the horrors in Brazil were insubstainable without a steady influx of human captives from Africa.
Consequentially, it's possible that the first peoples of America would survive in greater numbers.
Not for good reasons however.
I suspect that slave raids against the inhabitants of the America's would become a part of life.
The effects on the developing culture of the European colonists, if they actually needed to confront the reality of raiding for slaves, are potentially drastic.
It's possible that it would force a faster abolition of slavery. In would like to believe that.
But, I can't help but suspect that it would harden society toward slavery, and make abolition harder.
It might even quash the enlightenment philosophy that has shaped so much of the past 200 years.
On the African continent itself, I suspect that the native populous would have a good amount of time to recover in the interior, but it probably wouldn't matter, since such an apocalyptic loss of people would take with it the labor needed to maintain organized society, and the knowledge that would allow them to thrive.
On the surface, the people's in the interior of Africa may seem primitive, but the knowledge they needed to utilize the plants, animals, seasonal patterns, and geological features are immense.
Lose the wrong person, and you lose the knowledge, and a loss of that many people would mean losing nearly everything.
Still, that changes nothing about how hostile the environment of the African interior is to outsiders.
I suspect that the Western coast would be settled to provide supply ports for European trade with the east.
The South would likely be settled by the Dutch as it was in otl, though the lack of available slave labor would make things difficult.
I think much of the East coast would be quickly settled by Arabs, who would likely step up and fill the slave market in the region by important slaves from India.
It's also possible, that a Chinese diaspora would settle in, or be brought to the region, since that was around the time that many immigrated to the east indies (I think).
Over all, Africa would likely seem ever more forbidding than in OTL. Without a native population to guide explorers, provide a stream of resources to entice outsiders, and provide labor to extract those resources, colonialism would seem utterly unfeasible from a financial prospective.
Obviously, the explorers who were motivated by missionary zeal, wouldn't have been as likely to explore Africa, if they didn't actually know if anyone lived there.
Yeah.
Overall, it's difficult to overstate just how influential Africa was in the past few centuries.