Makarova and Soares committed to the tournament at the last minute and the unseeded duo rode the partnership to a grand slam triumph when Peschke failed to return a baseline backhand from Makarova to end their tie-break 12-10 after splitting the first two sets 6-7 6-1.
"The best feeling," said Soares, who became the first South American men's player to win the event after coming from a set down and facing a championship point at 9-10 in the tie-break.
Soares played two grand slam events last year with Makarova but had since teamed up with Australian Jarmila Gajdosova, with whom he played the last four grand slams.
But as the entry deadline time approached, the Brazilian found he would not gain direct entry into the field because his combined ranking with Gajdosova was too low.
Makarova, a mixed doubles runner-up with Jaroslav Levinsky at the 2010 Australian Open, had asked Soares about competing at Flushing Meadows but he told her he was already committed.
"A couple minutes before the sign-in, I thought I was out with Gajdosova and I started (thinking about) Katia, because with her I would be in," said Soares.
"Five minutes to go, I'm here in the referee's office and I find out Katia is practicing in the park. My coach went running all the way over there and talked to her and called me with like 30 seconds to go and said, 'You can sign.'
"So very last minute, 11:59, I signed us in. I guess it worked out."