df1             df2

id value        id value
 a     5         a   3
 c     9         b   7
 d     4         c   6
 f     2         d   8
                 e   2
                 f   1

df3
id value
a      5
b      7
c      9
d      4
e      2
f      2

In [80]: df1.set_index('id').combine_first(df2.set_index('id')).reset_index()
Out[80]:
  id  value
0  a    5.0
1  b    7.0
2  c    9.0
3  d    4.0
4  e    2.0
5  f    2.0

df1 = pd.DataFrame({'id': ['a', 'c', 'd', 'f'], 'value': [5, 9, 4, 2]})
df2 = pd.DataFrame({'id': ['a', 'b', 'c', 'd', 'e', 'f'], 'value': [3, 7, 6, 8, 2, 1]})
result = pd.merge(df2, df1, on='id', how='left', suffixes=('_x', ''))
result['value'] = result['value'].fillna(result['value_x'])
result = result[['id', 'value']]
print(result)