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.
PTI
Find the best IPL odds at 10Cric! Bet on all matches directly from your mobile phone.
Play casino in India at 7Jackpots, and enjoy real money games with fast and secure withdrawal options.