The alleged rape happened earlier this month in a school east of Johannesburg in front of other pupils who filmed the incident on their phones.
Prosecutors said rape charges were dropped because of a lack of evidence.
However, the National Prosecuting Authority (NPA) said it had decided all three could be charged under South Africa's Sexual Offences Act, which outlaws consensual sex with a minor.
The Children's Right Project, a legal advice group at the Western Cape University, said taking the matter to trial would not serve the girl's interests.
"There are other ways to handle to matter, the prosecutors are sending a horrific and harmful message to other rape survivors. That causes great concern," the group's Lorenzo Wakefield told BBC News.