The fifth-seeded Indian pair, playing their fourth final of the season, struggled past the Pakistan-Dutch combination 7-6 (6), 6-3 in the summit clash which lasted one hour and 24 minutes.
Bhupathi and Bopanna had won the Dubai ATP event and ended runners-up at Cincinnati and Shanghai.
The Indians could not convert a single breakpoint of the six chances in the opening set but held nerves in the tie-breaker to take the lead.
They saved a crucial break chance in the second set and cashed in on both the chances on opponents' serve to seal the win. The Indians have already qualified for the season-ending finale, where they will make their debut as a pair.
The 38-year-old Bhupathi is a four-time runner-up at the event, losing the final in 2010 with Max Mirnyi and 1997, '99 and 2000 with Leander Paes.
Bopanna, 32, made his debut at the year-end championships last year with Qureshi.