Highlighting the difference between two DataFrames

It is possible to use the DataFrame style property to highlight the background color of the cells where there is a difference.

Using the example data from the original question

The first step is to concatenate the DataFrames horizontally with the concat function and distinguish each frame with the keys parameter:

df_all = pd.concat([df.set_index('id'), df2.set_index('id')], 
                   axis='columns', keys=['First', 'Second'])
df_all

It's probably easier to swap the column levels and put the same column names next to each other:

df_final = df_all.swaplevel(axis='columns')[df.columns[1:]]
df_final

Now, its much easier to spot the differences in the frames. But, we can go further and use the style property to highlight the cells that are different. We define a custom function to do this which you can see in this part of the documentation.

def highlight_diff(data, color='yellow'):
    attr = 'background-color: {}'.format(color)
    other = data.xs('First', axis='columns', level=-1)
    return pd.DataFrame(np.where(data.ne(other, level=0), attr, ''),
                        index=data.index, columns=data.columns)

df_final.style.apply(highlight_diff, axis=None)

This will highlight cells that both have missing values. You can either fill them or provide extra logic so that they don't get highlighted.