Bopanna, ranked 10th in the world, had picked world number 125 Saketh Myneni as his preferred partner, putting in doubt the fate of Paes, who last week won the French Open mixed doubles title with Martina Hingis.
"Committee decided that the best bet for Indian tennis to win a medal at the Olympics would be Leander Paes and Rohan Bopanna," AITA chief Anil Khanna told reporters.
Bopanna said he admired Paes, who won a singles bronze medal at the Atlanta Games in 1996, but believed their styles of play were not complementary.
"The AITA Selection Committee has now made its decision after due consideration of my representation... I respect this decision and look forward to participating in Rio," Bopanna said in a statement.
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Bopanna will pair up with Sania Mirza, the world's top-ranked women's double player, in the mixed doubles in Rio.
(Reporting by Sudipto Ganguly; editing by Ed Osmond)
