In this Letter, we manipulate the phase shift of a Josephson junction using a parallel double quantum dot (QD). By employing a superconducting quantum interference device, we determine how orbital hybridization and detuning affect the current-phase relation in the Coulomb blockade regime. For weak hybridization between the QDs, we find π junction characteristics if at least one QD has an unpaired electron. Notably the critical current is higher when both QDs have an odd electron occupation. By increasing the inter-QD hybridization the critical current is reduced, until eventually a π-0 transition occurs. A similar transition appears when detuning the QD levels at finite hybridization. Based on a zero-bandwidth model, we argue that both cases of phase-shift transitions can be understood considering an increased weight of states with a double occupancy in the ground state and with the Cooper pair transport dominated by local Andreev reflection.