The paper proposes an approach to numerical simulation of shock waves in rarefied gas mixtures on the basis of direct solution of the Boltzmann kinetic equation. Software for simulating the gas flows was developed. The structure of a shock wave in a binary gas mixture was computed with an accuracy controlled by the computational parameters. The computations were performed for various molecular masses ratios and Mach numbers. The total accuracy of at least 1.4% for the local values of the molecular densities and temperatures of the mixture components was achieved. Numerical simulation of a shock wave propagation through a periodically perforated surface was performed. The distributions of the macroscopic characteristics of the mixture components at various points in time were obtained. Unsteady areas of strong separation of the gas mixture components were discovered.