barrier of Josephson junctions. Amorphous Al2O3 is widely used as a barrier material, but under irradiation, oxygen vacancy (VO) defects are readily generated, introducing noise sources that accelerate qubit decoherence. We systematically investigate the structural characteristics and electronic impact of VO defects in amorphous Al2O3 using first-principles calculations and \textit{ab initio} molecular dynamics. Our results show that both the coordination environment and concentration of VOs strongly influence electrical conductivity. In particular, two- and three-coordinated VOs, unique to the amorphous structure, enhance conductivity more than conventional four-coordinated vacancies. Increasing VO concentration amplifies conductivity fluctuations, which we link to critical current noise in Josephson junctions. Using a noise model, we estimate that higher VO densities lead to shorter qubit coherence times. These findings provide insights for radiation-hard design of superconducting quantum devices.