We theoretically study bound states generated by magnetic impurities within conventional s-wave superconductors, both analytically and numerically. In determining the effect of the hybridization of two such bound states on the energy spectrum as a function of magnetic exchange coupling, relative angle of magnetization, and distance between impurities, we find that quantum phase transitions can be modulated by each of these parameters. Accompanying such transitions, there is a change in the preferred spin configuration of the impurities. Although the interaction between the impurity spins is overwhelmingly dominated by the quasiparticle contribution, the ground state of the system is determined by the bound-state energies. Self-consistently calculating the superconducting order parameter, we find a discontinuity when the system undergoes a quantum phase transition as indicated by the bound-state energies.