The second-seeded Thais upset top-seeded and world No.4 pair Mathias Boe and Carsten Mogensen of Denmark 21-17, 15-21, 21-18 in 52 minutes.
Ranked 18th in the world, Maneepong and Nipitphon are among Thai hopefuls at the 17th Asian Games in Incheon, South Korea in September.
"They have played together quite well lately and we hope they will reach their peak at the Asian Games," said national coach Sompol Kookasemkij.
But he admitted there were a lot of good players standing in their way at the Incheon Games.
"The US Open win will boost their confidence ahead of a tougher task at the Asian Games," he said.
The duo will next play at the World Championships in Denmark from Aug 25-31.
However, their win at the US Open was Thailand's only success in three finals.
In the mixed doubles, top seeds Maneepong and Sapsiree Taerattanachai lost to Indonesia's unseeded Muhammad Rijal and Vita Marissa 21-16, 21-19 in 37 minutes.
In the women's doubles, third seeds Puttita Supajirakul and Sapsiree lost to unseeded Marissa and Shendy Puspa Irawati of Indonesia 21-15, 21-10 in only 29 minutes. Bangkok Post