The electronic structure of Sr3CuIrO6, a model system for the 5d Ir ion in an octahedral environment, is studied through a combination of resonant inelastic x-ray scattering and theoretical calculations. Resonant inelastic x-ray scattering spectra at the Ir L3 edge reveal an Ir t(2g) manifold that is split into three levels, in contrast to the expectations of the strong spin-orbit-coupling limit. Effective Hamiltonian and ab inito quantum chemistry calculations find a strikingly large noncubic crystal field splitting comparable to the spin-orbit coupling, which results in a strong mixing of the j(eff)=1/2 and j(eff)=3/2 states and modifies the isotropic wave functions on which many theoretical models are based.