The atomically precise engineering of impurities in graphene and the understanding of their structural and carrier-dependent electronic properties at the nanoscale are crucial for development of graphene-based nanoelectronics, catalytic, and energy technologies. Here, we report the controllable and reproducible incorporation of oxygen (O) substitutions into graphene using low-energy O+ ion implantation. This approach enables the selective incorporation of the otherwise elusive threefold-coordinated O substitutions, at a level far exceeding what has previously been attainable. Using complementary high-resolution scanning probe microscopy techniques and first-principles calculations, we resolve both the structural and electronic properties of the O-related defects. Specifically, scanning tunneling microscopy, together with chemical bond-resolved non-contact atomic force microscopy using a functionalized tip, provides unambiguous evidence for the existence and local atomic structure of threefold-coordinated O sites. Scanning tunneling microscopy and spectroscopy measurements, corroborated by density functional theory calculations, uncover characteristic impurity state that is energetically pinned to the Dirac point across different charge-carrier doping regimes. Our results not only establish a viable route for the deterministic incorporation of threefold-coordinated O dopants into graphene but also unveil their structural and electronic characteristics as a new class of atomically well-defined sp2-hybridized impurity in graphene.