Create two separate series for the chart by adding two columns, 1 for the 0's and one for the 1's. Use a formula like this one to get the data from column B (column C contains the 0's and 1's):
=IF(C2=0,B2,NA())
and the other new column:
=IF(C2=1,B2,NA())
Now use these two columns for Y-values, replacing the original one. This enables you to set a separate color for each of them.