The unseeded duo has started strongly before going down 6-4, 3-6, 3-10 to the fourth seeded Romanian-Dutch pair of Horia Tecau and Jean-Julien Rojer.
Bopanna and Matkowski were off to a strong start, forcing a service break in the fifth game of the opening set and held on to the advantage to take the lead.
But in the second game, Horia Tecau and Jean-Julien Rojer had continued their super tie-break to clinch the match and win the title.
Bopanna and Matkowski had made it to the final after beating Leander Paes and Guillermo Garcia-Lopez.