I suppose that there are two easier ways:
1) Following portuguese missionary activity, either Kongo or Ethiopia adhere to Catholicism and stick on it, becoming significant Catholic countries. They develop a local clergy (faster in Ethiopia, that had one already) that gradually makes its way into the Roman high clergy. At some point, an African cardinal is seen as politically the best choice, probably due to some some standstill in election, and becomes Pope as a compromise figure.
2) Some descendant of black slaves brought to Europe manages to ascend the clerical stair till the very top due to his sheer ability to do so. He could be for example an illegitimate son of some Italian Noble and a (former) slave maid of his. This would be regarded as shameful, but if the father gets him educated and he's smart enough, it could be not impossible. Illegitimate offspring of noblemen was disposed of that way in several cases.