The effect of seepage on the bearing capacity of soils was investigated by different researchers, while this special subject in the field of rock foundations has not been thoroughly investigated by researchers. Moreover, rock foundations are commonly required for large structures, like bridges and dams in which, seepage forces exist. Because of the complicated loading conditions of such large structures, using the simple available 2D methods for determining the bearing capacity may not give accurate results. In this paper, the ultimate bearing capacity of rock masses subjected to loads of gravity dams was investigated using the 3D finite element method. A case study of the Shafaroud concrete dam, which is under construction on a rock mass, was considered and the effect of seepage through the rock foundation was investigated using the numerical models. The bearing capacity was obtained by applying incremental stress to the bedding rock mass. For improving the accuracy of the obtained bearing capacity, the area of the rock mass in contact with the dam base was divided into some parts and uniform incremental stresses were applied to each part. This method resulted in the highest possible accuracy in obtaining the bearing capacity of dam foundations. The comparison of the obtained results and the available solutions showed good conformity among them. The suggested method is an appropriate guideline for determining the ultimate bearing capacity of foundations with complicated geometry and loading conditions.