Bopanna and his Pakistani partner, seeded third, faced stiff resistance from Trat Huey of Philippines and Briton Dominic Inglot before prevailing 6-7(3) 7-6(5) 10-3 in the quarter-finals.
They now face giant-killers Lukas Rosol and Joao Sousa, who dumped the top seeded American pair of Mike and Bob Bryan 3-6 6-3 14-12 in their quarter-final.
For Paes, it has been a nightmarish start to the new season. At the Chennai Open, he did not get to play a single ball as his partner Fabio Fognini pulled out due to an injury.
After losing the first set, Paes and Stepanek saved a break in the opening game of the second set off the Czech's serve. They had a chance to break their opponents in the next game but the Frenchmen saved.
Paes and Stepanek were leading 2-1 when rain forced suspension of play for about 45 minutes.
The Indian was broken in the seventh game which handed an opening to Benneteau and Roger-Vasselin, who extended their lead to 5-3 by holding serve in the next.
The winners will now take on Australian pair of James Duckworth and Samuel Groth.
Paes now heads to the season's first Grand Slam, the Australian Open, without much match practice.
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