The man had run to the guard room after students at the University of Technology in Kingston said they found him in a "compromising position" with another man in a campus bathroom on Thursday, the Jamaica Observer reported.
The other man managed to escape.
Once in the guard room, two security guards "physically assaulted" him as several other students "encircled the guard room attempting to get hold of the student," said a statement issued by the university, the guards' employer, Marksman Security Limited, and the university's student union.
The man was eventually removed from the campus by campus security and police.
The guards who allegedly beat the student did not uphold the security company's "contractual arrangements and ongoing mandate" to protect life and property, Robert Epstein, Guardsman's managing director, said late Friday afternoon in a statement.
The statement did not say what might happen to two other guards on duty at the time of the assault.
Homosexuality is illegal in Jamaica.