The top-seeded Indo-Swiss team outplayed the fourth seed team of Casey Dellacqua and Yaroslava Shvedova 6-3 6-3 in the final, which never rose to great heights.
Sania's win capped off a memorable US Open for Indians as Leander Paes had won the mixed doubles trophy with Hingis yesterday, in a repeat show of the Wimbledon.
Kazakshtan's Shvedova and Australia's Dellacqua struggled to hold serve, making it too easy for Sania and Hingis. The contest was over in just 70 minutes as the top seeds asserted themselves.
It was Sania and Hingis' second Major title in a row, having won the Wimbledon championships earlier this season.
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Sania now has five Grand Slam titles in her collection. She won three Mixed Doubles trophies, the last one coming at this very venue with Bruno Soares in 2014.
In an extraordinary season, Hingis has won five Grand Slam titles this season, taking her overall number to 20. She won three titles with Paes and two with Sania.
"It's a great year for us. Already been a great year, became world number one. We were a solid team and were in with a chance in all Slams. We are happy to come through. I won mixed doubles here last year, great to come bak and win this," Sania said after her win.
Shvedova committed a double fault in the second game at 30-all to give top seeds a break point and then a superb return from Sania brought another opportunity but the fourth seeds saved both chances.
The top seeds did not have to wait much for next chance as they broke Dellacqua at love to take a 3-1 lead. But the advantage slipped soon as Sania was broken in the fifth.
Shvedova was far from the player she is as she was down by three break points in the very first game of the second set. Top seeds grabbed the opportunity and consolidated lead with a solid hold.
Sania fired two stunning service winners on Dellacqua's serve as the Australian was broken at love in the seventh game.
Hingis hit an overhead volley winner on the first match point after Shvedova's double fault at 40-all.