Christianity did not almost completely eradicate various indigenous systems of African spirituality. Many of those systems were not formal organized religions but instead a series of everyday practices and assumptions about the world which continue to inform the lives of many people in sub-Saharan Africa. Practicioners associated with those practices and assumptions continue to operate in many countries where Africans are also members of Christian congregations, and many African Christians move relatively seamlessly between both spiritual systems. For example, in contemporary South Africa, even though many people belong to Christian or Christian-inspired congregations, they also consult with indigenous healers (sangoma, inyanga).
Moreover, in those cases where indigenous systems of African spirituality actually were organized into formal institutions, those survive in many cases with considerable vigor right alongside Christianity. Yoruba religion in Nigeria and vodun in Benin are only two of a number of examples.
Many Christian congregations in sub-Saharan Africa are also what scholars of religion call "syncretic", meaning they have incorporated substantial proportions of indigenous African spiritual ideas and practices. Sometimes to the point that it is more proper to put it the other way round--there are churches and movements that are really African indigenous spiritual systems that have incorporated some elements of Christianity, such as Kimbanguism in the Democratic Republic of Congo, the Vapostori of Zimbabwe, or the Zion Christian Church in South Africa.
If we're talking the whole of sub-Saharan Africa, it's also important to note that Christianity was present in Ethiopia pretty much from the religion's beginnings, having been adopted as the state religion of the kingdom of Axum in the early 300s. Meaning that in the broadest sense the religion is not a sudden latecomer associated exclusively with missionaries from Europe.
However, in terms of missionaries and colonial policy in the 19th and early 20th Century, many British and French colonial officials argued that it was important to restrict missionaries from working in Muslim communities in West and East Africa on the grounds that Muslims were likely to take offense at their activities and be provoked to unrest. To some extent this was one of the lessons that British officials took from the Indian Mutiny--that adherents of formal organized religions other than Christianity were likely to strenuously resist intrusions on their religious practices. The French came to similar conclusions in their colonial administrations in North Africa and the Middle East. Some colonial officials like Frederick Lugard even argued that Islamic authorities and chiefs made the best proxies for European imperial power and should be actively solicited as allies, sometimes citing imagined racial or civilizational hierarchies to support their opinion. There were colonial officials and some missionaries who pointedly disagreed with this position, but they rarely acted on their disagreement. To a significant extent, this put Muslim communities in sub-Saharan Africa in a situation that strengthened or protected their religious affiliations.