Hydroxyapatite (HA) can be used in odontology and orthopedic grafts to restore damaged bone due to its stable chemical characteristics, composition, and crystal structural affinity for human bone. A three-step hydrothermal method was used for the extraction of biogenic calcined HA from the buffalo waste bones at 700 °C (HA-700) and 1000 °C (HA-1000). Extracts were analyzed by thermogravimetric analysis, differential scanning calorimetry, X-ray fluorescence, X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, and in vivo examination of HA xenografts for femoral lesions in experimental rats. Crystallinity, purity, and morphology patterns showed that the HA main phase purity was 84.68% for HA-700 and 88.99% for HA-1000. Spherical HA nanoparticles were present for calcined HA-700 samples in the range 57–423 nm. Rats with critical bone lesions of 3 mm in diameter in the left femur treated with calcined HA-700 nanoparticles healed significantly (p < 0.001) faster than rats treated with HA-1000 or negative controls. These findings showed that spherical biogenic HA-700 NPs with a bud-like structure have the potential to stimulate both osteoconduction and bone remodeling, leading to greater bone formation potential in vivo. Thus, the calcined biogenic HA generated from buffalo waste bones may be a practical tool for biomedical applications.