Depth-induced spherical aberration in three-dimensional (3D) microscopy causes the 3D system response to vary with imaging depth within the sample. In order to overcome restoration artifacts, depth-variant restoration algorithms have been developed, which are computationally intensive. In this paper, we present an approach based on wavefront encoding that enables restoration of images from a thick object using a space-invariant algorithm. Experimental validation of an imaging system in which the pupil is modified by a phase mask, thereby rendering the point spread function less sensitive to imaging depth is demonstrated. Simulated results using a 63X/1.4 NA oil immersion microscope objective lens show that it is possible to restore images of a 30 µm thick sample using a SI approach with reduced artifacts compared to restorations of images from the conventional system. Our results are validated using experimental images.