"It's always tough to play against friends," Bopanna said. "Then, I also want to thank my partner. He wasn't feeling well this morning but he came out and played a great match."
Break points savedThe second seeds saved all the four breakpoints they faced in the match before prevailing in the second-set tie-breaker. It was Bopanna's eighth ATP doubles title.
The Indian has recently been ignored for the Davis Cup tie against Indonesia in April.
Last year he won two titles - Paris Masters and Dubai event - with compatriot Mahesh Bhupathi.
Bopanna and Fleming shared €29,000 as prize money and earned 250 ranking points each.
This was the Briton's second title this season.