Defects in graphene are important nanoscale pathways for metal atoms to enter the interface between epitaxial graphene and SiC in order to form stable ultrathin metal layers with new exotic physical properties. However, the atomic-scale details of defects that mainly govern the intercalation process remain modest. In this work, we present the first atomic investigation of point defects generated by oxygen plasma treatment on epitaxial graphene grown on SiC using low-temperature scanning tunneling microscopy, corroborated by density functional theory calculations. We found a broad spectrum of point defects that varies in size, shape, and symmetry and is dominated by triangular species. Tunneling spectroscopy identified defect-induced states in the vicinity of the Fermi level that significantly perturb the graphene electronic properties at the defect site. Based on the well-defined defect symmetry, we simulated the local density of states of the triangular defects and their corresponding scanning tunneling microscopy images which further helped us to identify the exact atomic configurations of monovacancy defects. The combination of atomic-scale scanning tunneling microscopy experiments and reliable density functional theory simulations provides ultimate microscopic details and opens a new way to identify the atomic configurations of defects in oxygen plasma-treated graphene. Our work might shed light on precise control of defect engineering in graphene for metal intercalation by controlling the defect types based on a deep understanding of each configuration. Display omitted