Bhupathi and Bopanna were bidding to win the season-ending event for the first time, but they were beaten by Spanish sixth seeds Marcel Granollers and Marc Lopez at London’s O2 Arena.
It was the fifth time 38-year-old Bhupathi had lost in the final.
But the duo, who won the Paris Masters earlier this month, won’t be able to have another run at the title next year after Bopanna confirmed they have decided to split.
Bopanna, 32, will play with American Rajeev Ram, while Bhupathi is yet to reveal his new partner.
Asked if they would continue playing together next season, Bopanna said: “No. We’re playing with different partners for the next season.
“I’m playing with Rajeev Ram next year. He comes to the tournament in Chennai every year. Just maybe a few days before Chennai we’re going to start. Tennis wise, we’ve had a great two weeks and can’t complain about that.”
Bhupathi added: “There were times in the year where, the pundits of Indian tennis threw us under the bus, said that we’re not good enough, said that these guys are jokers. We’ve beaten all the top teams there are to beat.”