In the beginning, computable functions were always total, but when where the partial functions included
The Stanford Encyclopaedia of Philosophy has a summary of the history of recursive functions. In particular, in Section 1.8 we can read that Stephen Kleene explicitly defined the partial recursive functions, and showed them to be equivalent to several other notions of computable functions, in a series of papers between 1936 and 1954. For example, already his 1936 paper General recursive functions and natural numbers introduces the unbounded search operator which leads to partial functions (when the search does not find anything).