A little slower, but readable I think:
>>> s, l, m
([5, 4, 3, 2, 1, 0], [0, 1, 3, 5], [0, 0, 0, 0])
>>> d = dict(zip(l, m))
>>> d #dict is better then using two list i think
{0: 0, 1: 0, 3: 0, 5: 0}
>>> [d.get(i, j) for i, j in enumerate(s)]
[0, 0, 3, 0, 1, 0]