Thabo Bester was at large for a year after it was thought he died by setting himself on fire in his prison cell.
A manhunt was launched last month after a new post-mortem investigation revealed the body was not actually his.
Bester was caught on Friday with his girlfriend and a third suspect and will be extradited to South Africa.
Police said they believe the trio was intending to flee into neighboring Kenya.
Bester is known as the “Facebook rapist” for using social networking site to lure his victims.
He was convicted in 2012 for the rape and murder of his model girlfriend Nomfundo Tyhulu. A year earlier, he was found guilty of raping and robbing two other women.
In May, it was reported he had been found dead in his cell after apparently setting himself on fire at the Mangaung Correctional Centre in the city of Bloemfontein.
However, local media began to raise doubts about Bester’s death late last year.
In March, police opened a new murder investigation after further tests revealed the deceased was not Bester – and that the unidentified person had died from blunt-force trauma to the head.
Employees of the British-owned security company G4S, which ran the prison where he was held, have been accused of helping him flee.
It has been said three employees were dismissed in connection with the incident.
Earlier this week, representatives for the organization failed to attend a meeting in parliament about Bester’s escape. The BBC has approached G4S for comment.
There have been many reported sightings of Bester over the past year, including claims he was grocery shopping in an affluent suburb of Johannesburg, and was living in a rented mansion there.
Bester’s escape sparked outrage in South Africa, which has one of the highest rates of sexual assault in the world.