Unseeded Bhupathi and Llodra downed the third seeded rivals 7-6 (6) 7-6 (6) in the fiercely fought final.
It was Bhupathi's fifth title in Dubai.
He first won the Dubai title in 1998 with Leander Paes, then again in 2004 with Fabrice Santoro, in 2008 with Mark Knowles and last year with compatriot Rohan Bopanna.