The BBC's Jon Leyne says the main objective of the opposition was to keep their movement alive.
He adds that the government and Mr Ahmadinejad must feel deeply frustrated, as they still have not silenced the protests, six months after claiming victory in the presidential election.
The disputed election led to the largest street protests since the 1979 Islamic Revolution, with thousands arrested and dozens killed.
The government then banned protests, so its opponents began using officially sanctioned demonstrations to turn out in big numbers and publicise their message.
Supreme leader berated
Monday's violence came during Iran's annual commemoration of the killings of three students during anti-American protests in 1953.
An Iranian activist describes how demonstrations are organised
At one university, students tore down a poster of Mr Ahmadinejad and trampled on it.
Elsewhere, in a highly unusual move, they chanted against the Supreme Leader, Ayatollah Ali Khamenei.
Police and members of the government's Basji militia tried to contain the protest within the universities. At the gates of Tehran university and several other universities, there were angry clashes.
As in previous protests, opposition supporters, some wearing green scarves and masks, chanted "Death to the Dictator". Green is the colour adopted by the reformist movement in recent months.
Iran's Irna state news agency said: "Some rioters who aimed at exploiting the special ceremonies to mark Student Day gathered in the streets surrounding Tehran University and clashed with law enforcement forces."
As protests were reported, Iranian state TV was broadcasting a round-table discussion about how loyal students are to the system.
OFFICIAL EVENTS USED FOR OPPOSITION PROTESTS
President Mahmoud Ahmadinejad sworn in, 5 August
Quds (Jerusalem) Day, 18 September
US embassy seizure anniversary, 4 November
Students Day, 7 December
Dozens of people have been given jail terms and as many as five people have been sentenced to death following the post-election demonstrations.
At the weekend, more than 20 people were arrested at a regular protest by a group of women that includes mothers whose sons and daughters were killed in post-election violence. Some of the women were later released.
On Sunday, former presidential candidate Mir Hossein Mousavi, who emerged as a leader for reformist opponents to the regime, said the protest movement was still alive.
In a statement posted on his website, he warned that authorities were "fighting with shadows in the streets".
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.