When two superconductors are connected across a ferromagnet, the spin configuration of the transferred Cooper pairs can be modulated due to magnetic exchange interaction. The resulting supercurrent can reverse its sign across the Josephson junction (JJ). Here we demonstrate Josephson phase modulation in van der Waals heterostructures when Cooper pairs from superconducting NbSe2 tunnel through atomically thin magnetic insulator (MI) Cr2Ge2Te6. Employing a superconducting quantum interference device based on MI JJs, we probe a doubly degenerate non-trivial JJ phase (ϕ) originating from the magnetic barrier. This ϕ-phase JJ is formed by momentum conserving tunneling of Ising Cooper pairs across magnetic domains in the Cr2Ge2Te6 barrier. The doubly degenerate ground states in MI JJs provide a two-level quantum system that can be utilized as a new disipationless component for superconducting quantum devices, including phase batteries, memories, and quantum Ratchets.