Two new methods for the investigation of two-dimensional quantum systems, whose Hamiltonians are not amenable to separation of variables, are proposed. The first one - SUSY-separation of variables - is based on the intertwining relations of higher-order SUSY quantum mechanics (HSUSY QM) with supercharges allowing separation of variables. The second one is a generalization of shape invariance. While in one dimension shape invariance allows us to solve algebraically a class of (exactly solvable) quantum problems, its generalization to higher dimensions has not been explored yet. Here we provide a formal framework in HSUSY QM for two-dimensional quantum mechanical systems for which shape invariance holds. Given the knowledge of one eigenvalue and eigenfunction, shape invariance allows us to construct a chain of new eigenfunctions and eigenvalues. These methods are applied to a two-dimensional quantum system, and partial explicit solvability is achieved in the sense that only part of the spectrum is found analytically and a limited set of eigenfunctions is constructed explicitly.