The seventh seeded Indian combo reached its second ATP World Tour Masters final of the season after beating British pair of Colin Fleming and Ross Hutchins 6-7 (4) 6-3 10-8 in an hour and 36 minutes.
While the fourth seeded Indo-Czech duo outplayed Marin Cilic of Croatia and Brazil's Marcelo Melo 6-0 6-2 in just 57 minutes.
In a hard-fought battle, Bhupathi and Bopanna came from a set down to make it to the final. The Indian pair could convert only one out of the six breakpoints opportunities to pocket the match.
Currently eighth in the ATP doubles team rankings race to London, Bhupathi and Bopanna are bidding to qualify for the Barclays ATP World Tour Finals by winning their second ATP World Tour title of the season, after victory at the Dubai Duty Free Tennis Championships.
Meanwhile Paes and Stepanek had an easy outing as they converted six of the seven breakpoints they got, while saving three out of four to walk away with the match.