The purpose of this research is to study the biomechanical response of dental implants in bone-level type locations, 0.5 mm above and below the bone level. In addition, the influence of the thickness of the cortical bone on osseointegration is determined due to the mechanical loads transfer from the dental implant to the cortical and trabecular bone. The thicknesses studied were 1.5 mm and 2.5 mm. Numerical simulations were performed using a finite element method (FEM)-based model. In order to verify the FEM model, the in silico results were compared with the results obtained from a histological analysis performed in an in vivo study with 30 New Zealand rabbits. FEM was performed using a computerized 3D model of bone-level dental implants inserted in the lower jawbone with an applied axial load of 100 N. The analysis was performed using different distances from the bone level and different thicknesses of cortical bone. The interface area of bone growth was evaluated by analyzing the bone–implant contact (BIC), region of interest (ROI) and total bone area (BAT) parameters obtained through an in vivo histological process and analyzed by scanning electron microscopy (SEM). Bone-level implants were inserted in the rabbit tibiae, with two implants placed per tibia. These parameters were evaluated after three or six weeks of implantation. FEM studies showed that placements 0.5 mm below the bone level presented lower values of stress distribution compared to the other studied placements. The lower levels of mechanical stress were then correlated with the in vivo studies, showing that this position presented the highest BIC value after three or six weeks of implantation. In this placement, vertical bone growth could be observed up the bone level. The smallest thickness of the study showed a better transfer of mechanical loads, which leads to a better osseointegration. In silico and in vivo results both concluded that the implants placed 0.5 mm below the cortical bone and with lower thicknesses presented the best biomechanical and histological behavior in terms of new bone formation, enhanced mechanical stability and optimum osseointegration.