Update index after sorting data-frame

df.sort() is deprecated, use df.sort_values(...): https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.sort_values.html

Then follow joris' answer by doing df.reset_index(drop=True)

You can reset the index using reset_index to get back a default index of 0, 1, 2, ..., n-1 (and use drop=True to indicate you want to drop the existing index instead of adding it as an additional column to your dataframe):

In [19]: df2 = df2.reset_index(drop=True)

In [20]: df2
Out[20]:
   x  y
0  0  0
1  0  1
2  0  2
3  1  0
4  1  1
5  1  2
6  2  0
7  2  1
8  2  2

Since pandas 1.0.0 df.sort_values has a new parameter ignore_index which does exactly what you need:

In [1]: df2 = df.sort_values(by=['x','y'],ignore_index=True)

In [2]: df2
Out[2]:
   x  y
0  0  0
1  0  1
2  0  2
3  1  0
4  1  1
5  1  2
6  2  0
7  2  1
8  2  2