Third seeds Paes and Dlouhy defeated fourth seeds Bhupathi, Paes' estranged partner, and Belarussian Mirnyi 6-2 7-5 in the final of the event, which is an ATP World Tour Masters 1000 tournament.
Paes and Dlouhy took an early 2-0 lead after winning points at deuce in the first two games and never let their opponents back into the first set.
The team also grabbed an early lead in the second set only to give it back when broken for 3-3. But Paes and Dlouhy broke back at 5-5 and then served out the match.
The winners of French Open and the US Open last year, Paes and Dlouhy were beaten finalists in Brisbane and Dubai earlier this season.
This was Paes' 43rd tour-level title while Dlouhy claimed his eighth.
"What's great actually about doing well this week is there's no pressure now for the rest of the clay court season. We've got to a final in Brisbane and got to quarters at the Aussie Open. Now there's no pressure. Now we're just playing for cream on the top," Paes said.
Dlouhy credited Paes for lifting the team when the chips were down.
"Playing with (Leander), it's always great because he has my back always. When I'm struggling with something, he's always with me on the same side and always tells me that nothing happened. We make it like a team. So it always helps you when you know that you are together, you are like brothers. That's the magic of the team, I think," he said.
Paes was runner-up at the Sony Ericsson Open in 2003 and 2007.