The unrest broke out after a group gathered at the Chahar-Bagh-e Bala near Isfahan University and blocked neighboring streets for several hours.
In the southern city of Shiraz, a few dozens converged at the Shahid Chamran boulevard around 22:30 (1800 GMT) and chanted incendiary slogans.
Some of the rioters used fire crackers and set tires on fire, trying to incite onlookers who watched them out of curiosity. The governor of Shiraz said the windows of several shops were smashed in the unrest.
In capital Tehran, a group of troublemakers gathered around a university dormitory before being dispersed by police.
Police on Sunday said that they had restored order in Tehran University's dormitory after several days of unrest and an unspecified number of people had been arrested.
The first unrest broke out on Tuesday following a peaceful gathering of students in protest to the alleged privatization of universities.
Officials have been quick to condemn the unrest and speculate that foreign hands were involved to orchestrate the protests with the help of "mercenaries".
On Thursday, Supreme Leader Ayatollah Ali Khamenei said that Washington was behind riots in the Islamic Republic and urged the nation and state officials to remain vigilant.
Washington has applauded the unrest, prompting Iran's Foreign Ministry spokesman Hamid Reza Asefi to come heavily on US and saying that American officials' statements constituted a "flagrant example of interference in Iran's internal affairs".
According to media, police have arrested several people, including plain-clothes vigilantes who have reportedly assailed student dormitories and beaten up students.
On Saturday, a student association, affiliated to volunteer Basij militia, warned 'vigilantes' against attacking students and their residences and said such raids could lead to playing to the hands of enemies.
"Such illegal actions are pursued along the lines of riots and ultimately benefit the enemies of the establishment," the Collegiate Basij Association of Tarbiat-e Modarres University said in a statement.
The association also hit out at the rioters, saying they were being incited by 'unknown hands and well-calculated suspicious currents' which, it said, sought to 'create riots by exploiting the sanctity of universities under the pretext of privatization'.
Meanwhile, the head of a key journalists association has written separate letters to Iran's interior minister and police chief, in which he has complained of alleged harassment of journalists by vigilantes during recent on-campus unrest.
Rajab-Ali Mazrouie, the head of the Iranian Journalists Guilds Association, has called for "respecting the prestige and dignity of journalists and guaranteeing their freedom of activity at the time of various events".
"In the course of student protests over the past few days, several journalists have been beaten up by plain-clothes elements as well as unfortunately by police," he said in a part of his letters, released Saturday.
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