Police have used pepper spray and stun guns on the third day of protests to try to disperse students, some of whom demonstrated topless on Tuesday.
A list of alleged campus rapists was leaked on social media on Sunday by a student group angered by assaults.
The university has suspended lectures and set up a task team to investigate.
The hashtags #RUReferencelist – referring to the 11 alleged rapists named on Facebook – and #nakedprotest have been trending on Twitter for a number of days in South Africa.
According to South African law, suspects in sex crimes can only be named after they have appeared in court and pleaded.
But students at the university in Grahamstown who say they have been victims of rape complain that no action was taken when they reported the assaults.
Vice-Chancellor Sizwe Mabizela called on all the students to come forward with information, saying the university had no record of such reports.
“As soon as we receive a statement, we will be able to hold a pre-suspension hearing with the accused with a view to suspend them,” South Africa’s ENCA broadcaster quoted him as saying.
Rhodes University’s student paper Activate says the arrested students are to be charged with protesting in public and being in possession of weapons.
A video on social media shows one student being arrested as police tried to remove a barricade erected on a road on campus.
South Africa has the highest number of rapes in the world – last year 43,195 cases were reported.
Officials claim the figures are on the decline, but activists say many more rapes go unreported.
source: BBC News