The paper suggests a generalization of the Sign-Perturbed Sums (SPS) finite sample system identification method for the identification of closed-loop observable stochastic linear systems in state-space form. The solution builds on the theory of matrix-variate regression and instrumental variable methods to construct distribution-free confidence regions for the state-space matrices. Both direct and indirect identification are studied, and the exactness as well as the strong consistency of the construction are proved. Furthermore, a new, computationally efficient ellipsoidal outer-approximation algorithm for the confidence regions is proposed. The new construction results in a semidefinite optimization problem which has an order-of-magnitude smaller number of constraints, as if one applied the ellipsoidal outer-approximation after vectorization. The effectiveness of the approach is also demonstrated empirically via a series of numerical experiments.