In this paper, a fourth-order dimensional nonlinear model is proposed for a diesel engine equipped with a Variable Geometry Turbocharger (VGT) and an Exhaust Gas Recirculation (EGR) valve. The referred model which takes into account the engine crankshaft speed dynamics and the air-path dynamics is a non-minimum phase unstable system. The fuel flow rate Wƒ which is considered as input for the engine crankshaft subsystem acts as an external perturbation for the three-order dimensional non-minimum phase air-path subsystem. The global control objectives are to track desired values of engine speed, intake manifold pressure and compressor flow mass rate which can be suitably chosen according to low emission criterions. For the considered objectives two loop based dynamical feedback stabilization control is proposed: an inner loop and an outer loop. The inner loop considers a control based on Lyapunov function which realizes the desired engine speed trajectory tracking. The outer loop concerns EGR & VGT control. It is developed from a particular extended nonlinear air-path subsystem with its modified outputs. This outer loop ensures both the desired intake manifold pressure and the desired compressor mass flow rate trajectory tracking. The outer loop dynamical feedback stabilization control provides also the external fuel mass flow rate perturbation rejection. The robustness and efficiency of the proposed method are demonstrated by simulation results.