We use classical results from harmonic analysis on matrix spaces to investigate the relation between the joint density of the singular values and of the eigenvalues of complex random matrices which are bi-unitarily invariant (also known as isotropic or unitary rotation invariant). We prove that one of these joint densities determines the other one. Moreover we construct an explicit formula relating both joint densities at finite matrix dimension. This relation covers probability densities as well as signed densities. With the help of this relation we derive general analytical relations among the corresponding kernels and biorthogonal functions for a specific class of polynomial ensembles. Furthermore we show how to generalize the relation between the eigenvalue and singular value statistics to certain situations when the ensemble is deformed by a term which breaks the bi-unitary invariance.