"This is a dispute between prisoners belonging to different gangs, who bring their conflicts with them when they are locked up," Rudy Esquivel, the prison spokesman said.
Police and prison authorities regained control of the jail on Saturday afternoon.
Pavoncito houses more than 900 prisoners convicted mostly of drug trafficking, murder and robbery.
Uprisings in overcrowded Central American prisons are frequent.
In May, inmates at the Chimaltenango prison in Guatemala decapitated a senior prison official during a riot that began after two women were caught smuggling drugs into the jail.
Guatemala is one of the most violent countries in Latin America and thousands of people are killed annually.
Its penitentiary system has been called corrupt, with gangs and drug traffickers often running their criminal empires from behind bars.