How about: df2.combine_first(df1)?
In [33]: df2
Out[33]:
A B C D
2000-01-03 0.638998 1.277361 0.193649 0.345063
2000-01-04 -0.816756 -1.711666 -1.155077 -0.678726
2000-01-05 0.435507 -0.025162 -1.112890 0.324111
2000-01-06 -0.210756 -1.027164 0.036664 0.884715
2000-01-07 -0.821631 -0.700394 -0.706505 1.193341
2000-01-10 1.015447 -0.909930 0.027548 0.258471
2000-01-11 -0.497239 -0.979071 -0.461560 0.447598
In [34]: df1
Out[34]:
A B C
2000-01-03 2.288863 0.188175 -0.040928
2000-01-04 0.159107 -0.666861 -0.551628
2000-01-05 -0.356838 -0.231036 -1.211446
2000-01-06 -0.866475 1.113018 -0.001483
2000-01-07 0.303269 0.021034 0.471715
2000-01-10 1.149815 0.686696 -1.230991
2000-01-11 -1.296118 -0.172950 -0.603887
2000-01-12 -1.034574 -0.523238 0.626968
2000-01-13 -0.193280 1.857499 -0.046383
2000-01-14 -1.043492 -0.820525 0.868685
In [35]: df2.comb
df2.combine df2.combineAdd df2.combine_first df2.combineMult
In [35]: df2.combine_first(df1)
Out[35]:
A B C D
2000-01-03 0.638998 1.277361 0.193649 0.345063
2000-01-04 -0.816756 -1.711666 -1.155077 -0.678726
2000-01-05 0.435507 -0.025162 -1.112890 0.324111
2000-01-06 -0.210756 -1.027164 0.036664 0.884715
2000-01-07 -0.821631 -0.700394 -0.706505 1.193341
2000-01-10 1.015447 -0.909930 0.027548 0.258471
2000-01-11 -0.497239 -0.979071 -0.461560 0.447598
2000-01-12 -1.034574 -0.523238 0.626968 NaN
2000-01-13 -0.193280 1.857499 -0.046383 NaN
2000-01-14 -1.043492 -0.820525 0.868685 NaN
Note that it takes the values from df1 for indices that do not overlap with df2. If this doesn’t do exactly what you want I would be willing to improve this function / add options to it.