At least 10 people were arrested, reported Reuters, and the state news agency IRNA said Mousavi and another defeated candidate from the disputed elections were forced to leave the rallies after being attacked by opponents.
According to the Associated Press, a reformist Web site reports that former Iranian president Mohammad Khatami, who emerged during the election dispute as a prominent pro-reform figure, was also reportedly attacked by the crowd and had to leave the event.
Khatami's brother, Mohammad Reza Khatami, told news agencies the former president was "not hurt."
"Some people shouted slogans against him," the brother told AFP. "He is home now. He is not hurt and he is fine."
Tens of thousands marched in the rallies, which in some areas became competing demonstrations by the opposition and government supporters. Opposition protesters chanted "death to the dictator," reported the Associated Press, and threw stones at security forces.
"Supporters of Ahmadinejad are beating supporters of Mousavi near the Vali-ye Asr street (in central Tehran). At least two protesters were injured," a witness told Reuters.
State television reported that moderate cleric Akbar Hashemi Rafsanjani, who also backed the opposition during the post-election political turmoil, had been replaced with a hard-line cleric to lead the prayers sermon at Tehran University on Friday, according to Reuters.
Opposition leaders contend that the June 12 election was fraudulent and have questioned the landslide victory that kept President Mahmoud Ahmadinejad in power, charges the government denies. Friday's protest was the first major opposition demonstration since mid-July.
The day of anti-Israel rallies, known as Quds Day, is one of the ways the Iranian government shows support for the Palestinians. Supreme Leader Ayatollah Ali Khamenei had barred anti-government demonstrations on Quds Day, which is held nationwide every year on the last Friday of the Muslim fasting month of Ramadan.
Ahmadinejad, who is set to address the United Nations in New York next week, renewed past controversial comments about the Holocaust during a speech for the rallies. He claimed it was a pretext for Israel's occupation of Palestinian lands.
"If the Holocaust was a real event, why don't they allow research on it to clear up facts," said Ahmadinejad, according to the AP.
He also said the "Zionists" are behind the ongoing wars in Afghanistan, Iraq and Sudan, reported the Los Angeles Times, and that Israel was created on "false and mythical claims."
In the past, Ahmadinejad's anti-Western speeches and comments on the Holocaust have caused an international outcry and further isolated Tehran, which is at loggerheads with world powers over its disputed nuclear program.
The comments came just weeks before scheduled talks between Iran and western powers. The discussions will also involve Britain, France, Germany, Russia and China.
Iran's continued defiance on the nuclear issue will lead to more isolation and economic pressure on Tehran, U.S. Secretary of State Hillary Clinton said in a speech Friday.
"There will be accompanying costs for Iran's continued defiance: more isolation and economic pressure, less possibility of progress for the people of Iran," Clinton said in remarks at the Brookings Institution.
"We have made clear our desire to resolve issues with Iran diplomatically. Iran must now decide whether to join us in this effort," Clinton said, according to the AP.
---- Compiled from wire reports and other media sources