We demonstrate that solvent vapor annealing of small molecular weight organic heterojunctions can be used to independently control the interface and bulk thin-film morphologies, thereby modifying charge transport and exciton dissociation in these structures. As an example, we anneal diphenyl-functionalized squaraine (DPSQ)/C(60) heterojunctions before or after the deposition of C(60). Solvent vapor annealing of DPSQ before C(60) deposition results in molecular order at the heterointerface. Organic photovoltaics based on this process have reduced open circuit voltages and power conversion efficiencies relative to as-cast devices. In contrast, annealing following C(60) deposition locks in interface disorder found in unannealed junctions while improving order in the thin-film bulk. This results in an increase in short circuit current by >30% while maintaining the open circuit voltage of the as-cast heterojunction device. These results are analyzed in terms of recombination dynamics at excitonic heterojunctions and demonstrate that the optimal organic photovoltaic morphology is characterized by interfacial disorder to minimize polaron-pair recombination, while improved crystallinity in the bulk increases exciton and charge transport efficiency in the active region.