This paper introduces a geometric Quaternion-based Unscented Particle Filter for Visual-Inertial Navigation (QUPF-VIN) specifically designed for a vehicle operating with six degrees of freedom (6 DoF). The proposed QUPF-VIN technique is quaternion-based capturing the inherently nonlinear nature of true navigation kinematics. The filter fuses data from a low-cost inertial measurement unit (IMU) and landmark observations obtained via a vision sensor. The QUPF-VIN is implemented in discrete form to ensure seamless integration with onboard inertial sensing systems. Designed for robustness in GPS-denied environments, the proposed method has been validated through experiments with real-world dataset involving an unmanned aerial vehicle (UAV) equipped with a 6-axis IMU and a stereo camera, operating with 6 DoF. The numerical results demonstrate that the QUPF-VIN provides superior tracking accuracy compared to ground truth data. Additionally, a comparative analysis with a standard Kalman filter-based navigation technique further highlights the enhanced performance of the QUPF-VIN.