The second seeded Indo-Pak pair fought gallantly before losing 6-7 (6) 6-7 (5) to their unseeded Italian rivals in one hour and 36 minutes.
The Indo-Pak Express though earned 150 ATP ranking points each which will help them stay in contention for a place in the season-ending and prestigious World Tour finals.
They are standing seventh in the top-ranked teams in the world and need to remain in top-eight to qualify.
With this defeat, Bopanna and Qureshi have now lost six of the seven ATP finals this season.
They won their first title in February at Johannesburg and have lost all six finals they made after that.
They lost the summit clashes of the US Open and New Haven event in August, Atlanta event in July, Nice event in May and Morocco event in April.