Вы можете использовать concat и drop_duplicates :
df1 = pd.DataFrame([["111", "aaa", "pune", "10000"],["222", "bbb", "pune", "20000"],["333", "ccc", "mumbai", "30000"],["444", "ddd", "pune", "40000"], ], columns=['emp_id', 'emp_name', 'City', 'Salary'])
df2 = pd.DataFrame([["111", "aaa", "pune", "60000"],["222", "bbb", "pune", "20000"],["333", "ccc", "mumbai", "30000"],["444", "eee", "pune", "40000"], ], columns=['emp_id', 'emp_name', 'City', 'Salary'])
print pd.concat([df2,df1]).drop_duplicates(keep=False).drop_duplicates(['emp_id'])
emp_id emp_name City Salary
111 aaa pune 60000
444 eee pune 40000