The fifth seed Indian pair, playing their fourth final of the season, struggled past the Pakistan-Dutch combination 7-6 (6) 6-3 in the summit clash, lasting 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 debut as a pair.
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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, had made his debut at the year-end championships last year with Qureshi.