Pandas convert datetime with a separate time zone column

Here is a vectorized approach (it will loop df.time_zone.nunique() times):

In [2]: t
Out[2]:
             datetime         time_zone
0 2016-09-19 01:29:13    America/Bogota
1 2016-09-19 02:16:04  America/New_York
2 2016-09-19 01:57:54      Africa/Cairo
3 2016-09-19 11:00:00    America/Bogota
4 2016-09-19 12:00:00  America/New_York
5 2016-09-19 13:00:00      Africa/Cairo

In [3]: for tz in t.time_zone.unique():
   ...:         mask = (t.time_zone == tz)
   ...:         t.loc[mask, 'datetime'] = \
   ...:             t.loc[mask, 'datetime'].dt.tz_localize(tz).dt.tz_convert('UTC')
   ...:

In [4]: t
Out[4]:
             datetime         time_zone
0 2016-09-19 06:29:13    America/Bogota
1 2016-09-19 06:16:04  America/New_York
2 2016-09-18 23:57:54      Africa/Cairo
3 2016-09-19 16:00:00    America/Bogota
4 2016-09-19 16:00:00  America/New_York
5 2016-09-19 11:00:00      Africa/Cairo

UPDATE:

In [12]: df['new'] = df.groupby('time_zone')['datetime'] \
                       .transform(lambda x: x.dt.tz_localize(x.name))

In [13]: df
Out[13]:
             datetime         time_zone                 new
0 2016-09-19 01:29:13    America/Bogota 2016-09-19 06:29:13
1 2016-09-19 02:16:04  America/New_York 2016-09-19 06:16:04
2 2016-09-19 01:57:54      Africa/Cairo 2016-09-18 23:57:54
3 2016-09-19 11:00:00    America/Bogota 2016-09-19 16:00:00
4 2016-09-19 12:00:00  America/New_York 2016-09-19 16:00:00
5 2016-09-19 13:00:00      Africa/Cairo 2016-09-19 11:00:00