We show that all self-adjoint extensions of semi-bounded Sturm-Liouville operators with limit-circle endpoint(s) can be obtained via an additive singular form bounded self-adjoint perturbation of rank equal to the deficiency indices, say d ∈ {1, 2}. This characterization generalizes the well-known analog for semi-bounded Sturm-Liouville operators with regular endpoints. Explicitly, every self-adjoint extension of the minimal operator can be written aswhere A 0 is a distinguished self-adjoint extension and Θ a self-adjoint linear relation in C d . The perturbation is singular in the sense that it does not belong to the underlying Hilbert space but is form bounded with respect to A 0 , i.e. it belongs to H −1 (A 0 ), with possible 'infinite coupling.' A boundary triple and compatible boundary pair for the symmetric operator are constructed to ensure the perturbation is well-defined and self-adjoint extensions are in a one-to-one correspondence with self-adjoint relations Θ. The merging of boundary triples with perturbation theory provides a more holistic view of the operator's matrix-valued spectral measures: identifying not just the location of the spectrum, but also certain directional information. As an example, self-adjoint extensions of the classical Jacobi differential equation (which has two limit-circle endpoints) are obtained and their spectra are analyzed with tools both from the theory of boundary triples and perturbation theory.