A South African judge acquitted Makopo on all charges, saying the prosecution failed to prove their case beyond a reasonable doubt.
The charges were made shortly after the school opened in Johannesburg in 2007. Winfrey was stunned by the allegations given her own history of childhood sexual abuse and vowed to make changes.
Winfrey has issued a statement praising the nine girls who testified at the trial.
"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.
Winfrey's $40 million school offers South African teenagers from deprived backgrounds the opportunity for a quality education in a country where schools still struggle 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.