In this paper, we show that the Eastern Nilotic language Bari exhibits extensive evidence for a pattern so far unattested in the phonological literature: suppletive allomorphy of tonal affixes which is sensitive to the number of syllables in the base word. Whereas ‘syllable-counting allomorphy’ (SCA) is amply attested for segmental affixes, there are no reported cases from tonal affixation (Paster 2005, 2006). A second unusual and theoretically significant property of Bari tonal allomorphy is that different allomorphs appear to be added at different stages of the morphophonological derivation, either before or after association and spreading of the lexical tone melodies of stems. We capture this in our analysis by adopting Stratal Optimality Theory (Kiparsky 2015, Bermúdez-Otero 2018) and the assumption that different allomorphs are specified to be inserted either at the Stem Level or the Word Level. Whereas it is a standard assumption in the stratal literature that different suppletive allomorphs of an inflectional category might have different stratal affiliations (see, e.g., Kiparsky 1982, Wiese 1988 on plural marking in Germanic), such a stratal split has so far not been documented for strictly phonologically sensitive allomorphy. Finally, we show that the Bari data also provide new evidence for two broader claims: the morphophonological independence of tonal morphology from segmental morphology, and the non-optimizing nature of phonologically conditioned suppletive allomorphy.