St. Lawrence County District Attorney Mary Rain said the girls turned up cold and wet but unharmed at a home in Richville, about 13 miles from where they disappeared in the rural town of Oswegatchie.
She said 12-year-old Fannie and 7-year-old Delila Miller were dropped off and knocked on the door, asking for help getting home. A neighbor who visited the Miller family after hearing word of the girls' return said she spoke with one of their brothers, who said they were well and being checked out.
There were no details immediately available on what happened to the girls or if there are suspects in their disappearance.
Word of their return came shortly after about 200 people attended a prayer vigil at Cornerstone Wesleyan Church in nearby Heuvelton.
The sisters vanished at about 7:30 p.m. Wednesday after a white car pulled up to the farm stand and they went down to tend to the customers while the rest of their family stayed at a barn for the evening milking.
Searchers had scoured far northern New York for the girls in a hunt hampered by the lack of photos of the girls for authorities to circulate among a frightened community.
The girls are among the youngest of Mose and Barb Miller's 13 children, who range in age from 1 to 21 years, neighbor Dot Simmons said.
The girls routinely took on the chore of selling the fruits, vegetables, jams and other products of the farm, Simmons said.
"It's absolutely amazing," she said of their return.
St. Lawrence County is home to New York's second-largest Amish population, which has grown in the past decade because of productive land and property prices lower than in Pennsylvania. The Amish are helping law enforcement get the word out the old-fashioned way by word of mouth.
Associated Press writer Chris Carola contributed to this report.