Language contact between migrating Bantu speakers and resident Khoisan speakers has resulted in the adoption of clicks in various southern African Bantu languages. This paper uses the comparative method to show that for one particular cluster of Bantu click languages, the Nguni languages, a large number of phonemic clicks can be reconstructed to its putative ancestor Proto-Nguni, including a palatal click rarely found in Bantu languages and no longer used as such in any living Nguni language. Although clicks have undergone subsequent developments in individual Nguni languages, no new click phonemes were acquired through language contact, showing that clicks were already present very early in the history of the Nguni languages. This relative chronology provides new insights into how the relations between Bantu- and Khoisan-speaking communities in southern Africa developed over time.