The fifth seed Indian pair, making its debut as a pair at the elite event, lost the title clash 5-7 6-3 3-10 to the sixth seeded combine in one hour and 30 minutes.
No Indian pair has ever won the year-end finale although Leander Paes and Bhupathi reached the finals thrice together.
Now it's fifth time that Bhupathi has ended runners-up at the event, where world's top-8 teams compete for the championship. With Paes he ended runners-up in 1997, 1999 and 2000 and with Max Mirnyi in 2010.
Bhupathi and Bopanna had beaten Paes and his Czech partner in the semifinals.
They end the 2012 season and their partnership with two titles -- Dubai and the Paris Masters.
Bhupathi will partner Daniel Nestor in the next season while Bopanna is yet to confirm his teammate for the next season.