The Uitenhage Regional Court sentenced Benjamin Jaggers, 18, to 18 years in prison and co-accused Neville Kock, 23, to nine years.
Lt-Col Priscilla Naidu could not explain the difference in their jail terms, and said she was still waiting for the full docket.
The two were convicted of raping a 16-year-old girl in 2011.
“The teenager was walking home in Tiryville, in Port Elizabeth, in July last year when she was attacked and raped at knifepoint,” she said.
Jaggers and Kock were arrested shortly afterwards.