Sabrina Allen went missing in 2002 at the age of four, and was rescued in the operation on Tuesday in the town of Estafeta Tlaxcala, some 90 miles (140 km) east of Mexico City.
She is now 17 years old.
"I am overjoyed that Sabrina has been found alive and is safe," said her father Greg Allen in a statement released by private eye firm Klein Investigations and Consulting, who helped track his daughter down.
"Our entire family would like to thank the investigators that made this happen," he added.
He had been given sole custody of his daughter when he divorced his wife Dara Marie Llorens in 2000. But she "knowingly abducted" the child during a weekend visit in April 2002, according to an affidavit.
One Mexican policeman was injured in the operation to rescue her, officials said, adding that both Allen and her mother were returned to the United States overnight.
The father added: "Our prayers go out to the Mexican Federal Police officer who was injured. We also would like to thank the Mexican government for their cooperation in this case.
"They never gave up," he said, also thanking the Federal Bureau of Investigation and US marshals who took part in the mission.