The fourth seeded Indo-Romanian pair lost the final 3-6 6-7(6) to the unseeded Brazilian-Briton pair on hour and 29 minutes.
Bopanna and Mergea had a good chance to stretch the match to a Super Tie-breaker by racing to a 4-0 lead in the second-set tie-breaker but allowed the rivals to come back and snatch the win.
They lost their serve twice in the opening set and squandered two break chances when the Soares and Murray served.
Bopanna had won the event last year with Canadian partner Daniel Nestor.
Nevertheless, Bopanna and Mergea will go into the Australian Open in good rhythm and touch.
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