The fifth seed Indo-French pair suffered a 6-7 (5) 6-3 4-10 against Croat-Brazil combo in one hour and 17 minutes.
There was no break in the opening set as Bopanna and his partner saved all five chances while their rivals saved the only one they faced.
In the second set, the Indo-French combine broke its rival pair twice after initially suffering a break even as they stretched the match to a super tie-breaker.
Losing points on crucial juncture cost Bopanna and Roger-Vasellin the match in the Super tie-breaker.
