In this article, we present a numerical iterative method for the solution of internal viscous and incompressible flows in real porous three-dimensional bodies at their pore scale. We use the penalized formulation of the problem involving velocity and vorticity: an operator splitting allows to split apart the diffusion (inherited from Stokes equation) and the penalization phenomena (which takes into account the solid matrix). By means of the numerical analysis of the splitting, we exhibit the penalization coefficient which is actually effective. This method allows to deal only with fast-evaluation operators, that is to say scaling at most as O(n log n) where n is the number of underlying grid points, such as straightforward computations of finite differences schemes or FFT solver. The numerical analysis and implementation solutions are presented, and validated on various digital rock physics geometries acquired by micro-tomography, using numerical and physical diagnostics. To enforce this validation, we also present permeability estimations of several porous samples. The simulation of transport of passive and active scalars is finally investigated in order to perform the practical upscaling to 1D models of transport and diffusion at the Darcy scale.