Background and Objectives: In the literature, spinal navigation and robot-assisted surgery improved screw placement accuracy, but the majority of studies only qualitatively report on screw positioning within the vertebra. We sought to evaluate screw placement accuracy in relation to a preoperative trajectory plan by three-dimensional quantification to elucidate technical benefits of navigation for lumbar pedicle screws. Materials and Methods: In 27 CT-navigated instrumentations for degenerative disease, a dedicated intraoperative 3D-trajectory plan was created for all screws. Final screw positions were defined on postoperative CT. Trajectory plans and final screw positions were co-registered and quantitatively compared computing minimal absolute differences (MAD) of screw head and tip points (mm) and screw axis (degree) in 3D-space, respectively. Differences were evaluated with consideration of the navigation target registration error. Clinical acceptability of screws was evaluated using the Gertzbein–Robbins (GR) classification. Results: Data included 140 screws covering levels L1-S1. While screw placement was clinically acceptable in all cases (GR grade A and B in 112 (80%) and 28 (20%) cases, respectively), implanted screws showed considerable deviation compared to the trajectory plan: Mean axis deviation was 6.3° ± 3.6°, screw head and tip points showed mean MAD of 5.2 ± 2.4 mm and 5.5 ± 2.7 mm, respectively. Deviations significantly exceeded the mean navigation registration error of 0.87 ± 0.22 mm (p < 0.001). Conclusions: Screw placement was clinically acceptable in all screws after navigated placement but nevertheless, considerable deviation in implanted screws was noted compared to the initial trajectory plan. Our data provides a 3D-quantitative benchmark for screw accuracy achievable by CT-navigation in routine spine surgery and suggests a framework for objective comparison of screw outcome after navigated or robot-assisted procedures. Factors contributing to screw deviations should be considered to assure optimal surgical results when applying navigation for spinal instrumentation.