The second seeded Indo-British pair edged past the top seeds 6-4 7-6 (3) in the summit clash of the euro 528135 hard court event.
Bopanna played with Fleming in the absence of regular partner Rajeev Ram.
The second seeds saved all the four breakpoints they faced in the match before prevailing in the second-set tie- breaker.
It was eighth ATP doubles title for Bopanna, who has been ignored for India's Davis Cup tie against Indonesia.
Last year he won two titles -- Paris Masters and Dubai event -- with compatriot Mahesh Bhupathi.
Bopanna and Fleming shared euro 29,000 as prize money and earned 250 ranking points each.