They will now be up against top-seeded American brothers Mike and Bob Bryan, who got the better of the 12th-seeded British pair of Colin Fleming and Jonathan Marray 7-6 (7), 6-4 in their quarterfinal match.
Paes and Stepanek started off well and broke their rivals twice, while holding their own serve, to clinch the opening set in just 33 minutes.
But they were stretched quite a bit in the remaining two sets which took almost an hour each to conclude.
In the second set, neither of the two teams conceded a single break point.
Even though Qureshi and Rojer committed three double faults but fought hard enough to equalise and keep themselves in the match.
The third set was also closely-contested but Paes and Stepanek converted an all-important break point while Qureshi and Rojer frittered away the only one they got as the Indo-Czech pair sealed the issue.