The notion of discriminantly separable polynomials of degree two in each of three variables has been recently introduced and related to a class of integrable dynamical systems. Explicit integration of such systems can be performed in a way similar to Kowalevski's original integration of the Kowalevski top. Here we present the role of discriminantly separable polynomials in integration of yet another well known integrable system, the so-called generalized Kowalevski top - the motion of a heavy rigid body about a fixed point in a double constant field. We present a novel way to obtain the separation variables for this system, based on the discriminantly separable polynomials.