Sania-Soares will take on the unseeded Yung-Jan Chan of Chinese Taipei and Britain's Ross Hutchins in the semifinals.
The Hyderabadi made the women's quarterfinals with Cara Black, defeating Czech-Serbian combine of Klara Koukalova and Jelena Jankovic 6-3 6-2.
The third seeds next play China's Yi-Fan Xu and Kazakhstan's Zarina Diyas. Sania has not won a title yet at the US Open.
However, Indian tennis veteran Paes had a forgettable outing.
He and his experienced men's doubles partner Radek Stepanek lost to Spain's Marcel Granollers and Marc Lopez 2-6 6-4 1-6 in the third round.
The 41-year-old teamed up with Zimbabwe veteran Cara Black in the mixed doubles.
The third seeds failed to get going against the American-Mexican partnership of Abigail Spears and Santiago Gonzalez, losing the quarterfinal 4-6 6-4 8-10 in the Super Tie-Break.
In the junior boys round one, Sumit Nagpal got past Viktor Durasovic of Norway 6-3 6-4.