The fourth seeded Indo-Czech pair demolished the second seeded Austria-Brazilian pair 6-1 in 6-3 in one hour and 12 minutes at Arthur Ashe stadium.
It was a perfect climax for Paes and Stepanek, who came into the US Open with title in Winston Salem Open, as they won their second major title together, having won Australian Open last year.
It was third US Open title for 40-year-old Paes and the previous two had also come with Czech partners. In 2006, the Indian won with Martin Damm and in 2009 with Lukas Dlouhy.
Last year at the US Open, Paes had ended runner-up with Stepanek, losing to Bryan brothers.
Now Paes has 14 major titles in his cupboard, including six mixed doubles trophies. Stepanek has two Grand Slam titles, both with Paes.
It was one of the most lop-sided US Open title match as Peya and Soares failed to put up a fight. They had no clue whatsoever on how to counter the rampaging Indo-Czech combine.
Peya also required a medical timeout for a back problem in the second set while trailing 1-3. Peya was in pain but did not give up and even went on to hold his serve in that game.
Paes hit a forehand winner to earn the championship point and then hit a backhand volley to seal the trophy win.
Paes and Stepanek 23 winners to eight of their rivals.
They won 66 points while Peya and Soares 40.
Paes acknowledged Stepanek's resilience as he came back well from a back surgery early this year.
"Find someone from Czech republic that's my advise to anyone who is looking for a doubles partner. They are hard working guys. I have to thank him. He had lot of adversities this season, coming out of injury and surgery it's amazing to stand here. I have to thank him," Paes said.
"It is no shame to lose to these guys," said Peya.