The fourth-seeded Indo-Romanian pair eked out a 5-7 6-2 10-7 win over the third seeded Austrian-Brazilian team in one hour and 11 minutes.
Bopanna and Mergea had the Madrid Masters last month.
Individually, it was fourth title of the season for Bopanna, having won trophies in Dubai and Sydeny with Canadian partner Daniel Nestor.
After losing the first set, following a break of serve, Bopanna and Mergea cam back strong as they did not face a single breakpoint in the second set and broke their rivals twice to force a Match tie Breaker.