The Indian pair lost to Sweden's Robert Lindstedt and Romania's Horia Tecau.
The sixth seed Indian pair lost 4-6 4-6 to the fourth-seeded rival team in the summit clash of the US$ 2,825,280 hard court event, late Sunday night.
Bhupathi and Bopanna were playing their second final of the season. They had won a title in a Dubai ATP event in February.
India's Leander Paes and Czech Radek Stepanek had bowed out in the second round.