The vastly more experienced Kono, 21, said: "I knew she was going to hit the greens and get it close, so I had to play my own game."
Kono was a member of the 2010 USA Curtis Cup Team and is playing in her 22nd USGA championship.
Meanwhile, defending champion Danielle Kang, 18, from California holed a 9-iron shot for an eagle to eliminate fellow American Emma Talley, 17, in the second round.
Kang's stellar shot on the 364-yard, par-4 14th hole ended the match, 6 and 4.
Ko was seeking to become the first woman from New Zealand to win the coveted title and follow in the footsteps of 2008 men's US Amateur Champion Danny Lee.
- NZPA