The third seeds edged past the fourth seeded French-Serbian combination 7-6(4) 7-6(2) after battling for one hour and 41 minutes.
"If you had asked me 10 years ago if we would win here again 10 years later, I would have started laughing that we''d still be playing," Paes said after the win.
"It's a great feeling to come back and win in the summer. We didn't have so much rhythm in Europe, but we managed to put it together this week. We've beaten some really big teams and are playing well. For us, it's a big confidence booster for the US Open, but we still have a lot of work to do there."
This is the third title of the season for the Indian Express as they had triumphed at the Sony Ericsson Open and Chennai Open. Neither team dropped serve in the match.
"They are the hottest team and we had to play our best match of the year to beat them. We served and volleyed great, and played an error free match. When we had chances, we took them," Bhupathi said
The French-Serbian duo were looking to win their third straight title, having won the Legg Mason Tennis Classic in Washington DC and the Rogers Cup in Montreal last week.
The defeat snapped their superb 11-match win streak.