The paper presents the results of application of linear parameter varying (LPV) decoupling control and a prefilter to improve the tracking performance in the air path of Diesel engines modeled as a quasi-LPV system. The proposed decoupling method benefits the multi-variable control of multi-input multi-output (MIMO) systems with variable operating conditions, variable parameters and nonlinear behavior. The results of this paper illustrate the reduced variability and performance enhancement of the two inputs (EGR valve effective area and VGT effective area) and two outputs (boost pressure and mass air flow) dynamic system of the air path of Diesel engines, where there is a significant coupling in the system dynamics. The proposed design method combines a prefilter (used to shape the reference input) with the LPV feedback control (based on an LPV decoupling method) proposed here to achieve the reference tracking with desired transient performance specifications. The prefilter is designed based on the closed-loop dynamics resulting from the LPV design, and a systematic input shaping prefilter design process is developed. The designed prefilter successfully extends the closed-loop bandwidth. Simulation results demonstrate the effectiveness of the input shaping prefilter. Moreover, the designed prefilter is structurally simple and computationally efficient.