The fifth seeded Indian pair halted the winning run of the Indo-Czech combination with a 4-6 6-1 12-10 win in the semifinals and in the process avenged the defeat of the Shanghai Masters final last month.
Paes had said that Shanghai final was a kind of grudge match after the Olympics selection drama when both Bhupathi and Bopanna had refused to pair with him.
Paes and Stepanek's third seed team was the only one to enter the semifinals unbeaten. They had topped the Group A with three wins from as many matches.
Bhupathi and Bopanna, who are making their debut at the finale as a pair, now have a chance to create history as no Indian has won the year-end championship since Vijay Amritraj's triumph in 1977.
The Indians will face the winners of the other semifinal between English-Danish combine of Jonathan Marray and Frederik Nielsen and Spaniards Marcel Granollers and Marc Lopez in Monday's championship match.