We report the defect-mediated modulation of optical properties in vertically aligned ZnO nanowires via a substrate-assisted Ga incorporation method. We find that Ga atoms were incorporated into a ZnO lattice via the diffusion of liquid Ga droplets from a GaAs substrate in which as-grown ZnO nanowires were placed face down on the GaAs substrate and annealed at 650 °C. Based on structural and compositional characterization, it was confirmed that the substrate-assisted incorporation of Ga can induce a high defect density in vertically aligned ZnO nanowires grown on a Si substrate. In addition, distinct differences in optical properties between as-grown and Ga-incorporated ZnO nanowires were found and discussed in terms of defect-mediated modifications of energy band states, which were associated with the generation and recombination of photoexcited carriers. Furthermore, it was clearly observed that for Ga-incorporated ZnO nanowires, the photocurrent rise and decay processes were slower and the photocurrents under UV illumination were significantly higher compared with as-grown nanowires.