Prosecutors had accused former school matron Tiny Virginia Makopo of trying to kiss and fondle girls at the school soon after it opened in 2007 outside Johannesburg.
Makopo also had been accused of assaulting one of the teens as well as a fellow supervisor.
Mthunzi Mhaga, a spokesman for South Africa's National Prosecuting Authority, said Monday that Makopo had been acquitted of the charges.
"The magistrate indicated that the state did not prove itself case beyond reasonable doubt on all the charges. We won't be appealing the judgment," Mhaga said.
Winfrey had called the allegations crushing given her own stated history of childhood sexual abuse and promised an overhaul of the school.
"I will forever be proud of the nine girls who testified with the courage and conviction to be heard," Winfrey said in a statement Monday.
The lavish $40 million Oprah Winfrey Leadership Academy for Girls, which opened in January 2007, aims to give girls from deprived backgrounds a quality education in a country where schools are struggling to overcome the legacy of apartheid.
The school is spread across a 22-acre campus with neat lawns and garden paths decorated with mosaics. It has computer and science labs, a library and a wellness center. The school is home to about 300 girls from across the country.
Winfrey said Monday that the school's staff "is committed to providing a nurturing educational environment so that all of our girls may continue to flourish. And they are indeed thriving."
In March, Winfrey had settled a defamation lawsuit filed in Philadelphia by the school's former headmistress, Nomvuyo Mzamane, who claimed Winfrey defamed her in remarks made in the wake of the 2007 sex-abuse scandal at the school.
Mzamane claimed that she was never told of any sexual abuse. However, Winfrey's lawyers said in a March pretrial memo that Mzamane failed to discipline Makopo despite her history of run-ins with students and fellow staff.
Mzamane said she had trouble finding a job after Winfrey stated she had "lost confidence" in her.
Lawyers for both sides in March said Winfrey and Mzamane met to resolve their differences out of court.
Associated Press writer Eric Naki in Johannesburg contributed to this report.