The teacher told detectives that a 13-year-old boy raped her while his friend held her down. Both boys had been kept behind for detention and were alone with the teacher in the classroom at the school in Southwark, south London.
A second teacher came to her aid after she was left on the classroom floor.
Her allegations came as teaching unions highlighted the growing incidence of violence faced by teachers in classrooms and launched a campaign to improve their safety.
The Metropolitan Police said that the investigation was continuing and denied a report on the incident had been sent to the Crown Prosecution Service.
Police sources on the inquiry indicated privately it was unlikely that further action would be taken because of the lack of evidence to corroborate the teacher's allegations. Forensic science evidence was inadequate to support her case.
Both boys and the teacher have remained at home since the alleged incident. Anyone under the age of 14 is deemed incapable of rape so the accused youths could only have been charged with indecent assault.