Bopanna and Qureshi lost all the three round-robin matches, which pushed the Indian to 11th, loss of one place.
Leander Paes (8) and Mahesh Bhupathi (7), who made the semifinals had their rankings unchanged.
In the team rankings, Paes and Bhupathi finished the season in fourth position, just ahead of Bopanna-Qureshi combination.
In the singles, Somdev Devvarman, who had aimed to break into top-50, ended in 84th position.
Sania Mirza, recovering from a knee injury, signed off the WTA season at number 87 the singles and 11 in the doubles list.
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