  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) [1-4]. Here we demonstrate Josephson phase
modulation in van der Waals heterostructures when Cooper pairs from
superconducting NbSe$_2$ tunnel through atomically thin magnetic insulator (MI)
Cr$_2$Ge$_2$Te$_6$. Employing a superconducting quantum interference device
based on MI JJs, we probe a doubly degenerate non-trivial JJ phase ($\phi$)
originating from the magnetic barrier. This $\phi$-phase JJ is formed by
momentum conserving tunneling of Ising Cooper pairs [5] across magnetic domains
in the Cr$_2$Ge$_2$Te$_6$ 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 [6], memories [7,8], and quantum Ratchets [9,10].
