The biological aging of titanium implants, marked by increased surface hydrophobicity and organic contamination, reduces bioactivity and delays osseointegration. A major challenge in implant dentistry is determining how to preserve surface hydrophilicity during storage, as conventional atmospheric conditions accelerate surface degradation. This pilot in vivo study aimed to evaluate ozone nanobubble water (NBW3) as a storage medium to prevent biological aging and enhance the early-stage osseointegration of glow discharge-treated titanium implants. Screw-type implants were stored in either NBW3 or atmospheric conditions and then implanted into femoral bone defects in Sprague Dawley rats. Removal torque testing, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and histological analysis of bone-to-implant contact (BIC) were performed 14 and 28 days post-implantation. At 14 days, the NBW3-stored implants demonstrated significantly higher removal torque (2.08 ± 0.12 vs. 1.37 ± 0.20 N·cm), BIC (65.74 ± 12.65% vs. 44.04 ± 14.25%), and Ca/P atomic ratio (1.20 ± 0.32 vs. 1.00 ± 0.22) than the controls. These differences were not observed at 28 days, indicating NBW3’s primary role in accelerating early osseointegration. The findings suggest that using NBW3 is a simple, effective approach to maintain implant surface bioactivity during storage, potentially improving clinical outcomes under early or immediate loading protocols.