The two veterans, seeded fourth, got past fifth seeds Aisam-Ul-Haq Qureshi and Jean-Julien Rojer 6-1, 6-7 (3), 6-4 at the Flushing Meadows Tuesday.
The Indo-Czech pair faces familiar combination of Bob Bryan and Mike Bryan in the semifinals. The top seeds from America beat Britain's Colin Fleming and Jonathan Marray 7-6 (7), 6-4 in another quarterfinal.
It was neck and neck between Paes and Stepanek against the Pakistan-Netherlands combine. The difference in the end was about making the better use of break point opportunities which the fourth seeds did well, converting three of their seven break points. Their opponents failed to break even once in a match lasting two hours and 26 minutes.
Paes has won the US Open twice, in 2006 and 2009 while finishing runners up four times. Paes and Stepanek lost the 2012 US Open final to Bryan Brothers.