You can tell np.random.shuffle
to act on the flattened version:
>>> a = np.arange(9).reshape((3,3))
>>> a
array([[0, 1, 2],
[3, 4, 5],
[6, 7, 8]])
>>> np.random.shuffle(a.flat)
>>> a
array([[3, 5, 8],
[7, 6, 2],
[1, 4, 0]])