Intrinsic defects created by chemically inert gas (Xe) ion implantation in vertically grown ZnO nanorods are studied by optical and X-ray absorption spectroscopy (XAS). The surface defects produced due to dynamic sputtering by ion beams control the fraction of O and Zn with ion fluence, which helps in tuning the optoelectronic properties. The forbidden Raman modes related to Zn interstitials and oxygen vacancies are observed because of the weak Fröhlich interaction, which arises due to disruption of the long-range lattice order. The evolution of the lattice disorder is identified by O K-edge and Zn K-edge scans of XAS. The hybridization strength between the O 2p and Zn 4p states increases with ion fluence and modulates the impact of intrinsic defects. The ion irradiation induced defects also construct intermediate defects bands which reduce the optical bandgap. Density functional theory (DFT) calculations are used to correlate the experimentally observed trend of bandgap narrowing with the origin of electronic states related to Zn interstitial and O vacancy defects within the forbidden energy gap in ZnO. Our finding can be beneficial to achieve enhanced conductivity in ZnO by accurately varying the intrinsic defects through ion irradiation, which may work as a tuning knob to control the optoelectronic properties of the system.