Witnesses said that dozens of people had been hospitalised after serious beatings by police and pro-government militia.
"Lots of guards on motorbikes closed in on us and beat us brutally," one protester said.
"As we were running away the Basiji [militia] were waiting in side alleys with batons, but people opened their doors to us trapped in alleys."
Another witness told Al Jazeera that police were turning people away from Revolution Square.
"The roads were pretty much blocked by the militia, they were out with retractable metal batons. It looked like they were very frantically trying to keep people from the area," he said.
"It got a bit frightening. From what I saw, some people were still going down [to the square] and some people were running away.
"But there are still people waiting around to find an opportune time to go down there."
Amateur video, purportedly of Saturday's protests, showed dozens of Iranians running down a street after police fired tear gas.
As the clashes took place, a suspected suicide bomber blew himself up outside the shrine of Ayatollah Ruhollah Khomeini, the leader of the Islamic revolution in 1979, injuring at least two people.
Al Jazeera's Alireza Ronaghi, reporting from Tehran, said that state television showed footage of protesters being arrested after trying to break the police lines in Revolution Square.
"They also quoted the head of Iran's police force as thanking the Iranian people for not taking to the streets and taking the police warnings seriously," he said.
Ronaghi said that the protests had largely been quelled by Saturday evening
"The presence of security forces were very high, they definitely wanted to take back the streets of Tehran ... right now I don't expect that many protesters are concentrated anywhere in Tehran," he said.
Earlier on Saturday, Mir Hossein Mousavi and Mehdi Karoubi had declined to meet the Guardian Council, Iran's highest legislative body, concerning 646 complaints of voting irregularities in the June 12 poll.
The council had called for a meeting to discuss the vote, which both Mousavi and Karoubi have said should be annulled.
State television quoted a council spokesman as saying that the Guardian Council had expressed its readiness to "randomly" recount up to 10 per cent of the ballots.
Mousavi later renewed his for the election results to be cancelled in a letter to the Guardian Council published on his website.
The contested result gave President Mahmoud Ahmadinejad a tally of about 63 per cent, to Mousavi's 34 per cent. The council has so far promised only to recount some ballots if irregularities are found.
Ronaghi said that it was likely that the meeting would bring only minor changes to the poll outcome.
|Khamenei, left, cautioned that the mass protests in Tehran must cease [AFP]
"I think the Guardian Council intends to review all of the complaints," he said.
"In some of those cases, there are some obvious irregularities and I am sure that they will be addressed. I'm sure some of the ballot boxes will be annulled and they will be deducted from the results.
"But ... I find it very unlikely that there will be major change in the final result."
The meeting comes a day after Ayatollah Ali Khamenei, Iran's supreme leader, backed Ahmadinejad's victory and cautioned that mass protests - which continued daily from the release of the poll results until Thursday - must cease.
Khamenei said in a sermon during Friday prayers at Tehran University that if the supporters of defeated candidates fail to halt the protests "they will be responsible for its consequences, and consequences of any chaos".
But an indication that resistance to the results would continue came before dawn in Tehran on Saturday as opposition supporters called "Death to the dictator" and "God is the greatest" from the rooftops.
Television crews are prevented from filming rallies and many non-Iranian journalists have been prohibited from working in the country.