About 3,000 police officers had been deployed in East Jerusalem and nearby villages after Hamas and other Palestinian groups called for action in response to the reopening of the Hurva synagogue.
The Hurva, considered by some people to to be one of Judaism's most sacred sites, reopened for the first time in 62 years on Monday in the Jewish quarter of Jerusalem's Old City.
The walled Old City is at the heart of the Israeli-Palestinian conflict, which makes the reopening of the synagogue controversial.
Moreover, al-Aqsa, Islam's third holiest site, and the Hurva are about just 700 metres apart.
Al Jazeera's Sherine Tadros, reporting from Essawiyya, said Palestinian protesters hurled stones at the Israeli border guards, who responded using stun grenades.
Al Jazeera's Sherine Tadros reports on the violent clashes in occupied East Jerusalem
Earlier, Adnan al-Husseini, the governor of East Jerusalem, told Al Jazeera from al-Aqsa mosque that only a few people had been able to attend prayers because of restrictions placed on movement by Israeli authorities.
"Also, many police are at the entrance of the Old City and the mosque and on the streets of the Old City. So movement is very difficult and very tense.
"People are trying to come to the mosque, the shops, their houses. And unfortunately the Israeli police are stopping them."
Israeli officials have limited access to al-Aqsa since Friday for security reasons.
Palestinian men under the age of 50 have not been allowed to enter the mosque.
Micky Rosenfeld, the Israeli police spokesperson, told Al Jazeera: "Throughout the morning we have been dealing with local disturbances. A group of 50 to 60 Palestinians who are causing riots.
"The rest of Jerusalem itself is absolutely quiet. The Temple Mount is closed to visitors and tourists.
"Our units are responding to small incidents in and around East Jerusalem."
The previous day, Khaled Meshaal, Hamas' political chief who is exiled in Syria, strongly condemned the ceremony.
He urged Palestinians in Jerusalem to "take serious measures to protect al-Aqsa mosque from destruction and Judaisation".
Meshaal also said that Palestinians in the Gaza Strip and the West Bank should "launch a campaign to protect Jerusalem and Islamic and Christian holy sites there".
An Israeli government decision to include two West Bank religious sites in a Jewish national heritage plan has already angered Palestinians and raised tensions in recent weeks.
The announcement last week of Israeli plans for new settler homes near East Jerusalem has further contributed to the unrest.
The US state department announced on Tuesday that George Mitchell, the US envoy to the region, who had been due to visit Israel, would not now do so before a meeting of the Middle East diplomatic Quartet in Moscow on Thursday.
Hillary Clinton, the secretary of state, said that Israel must prove it is committed to the peace process with actions.
But she brushed aside suggestions that US relations with Israel are in crisis over the settlement announcement, made in the middle of a visit by Joe Biden, the US vice-president.
"We have an absolute commitment to Israel's security. We have a close, unshakable bond between the United States and Israel," she said.
Clinton also said she remained confident Mitchell would return soon and begin shuttling between the Israelis and Palestinians.
Message from Abbas
Meanwhile, Saeb Erekat, the chief Palestinian negotiator, left for Moscow on Tuesday to present the Quartet - which includes the US, Russia, the EU and the UN - with Palestinian conditions for starting peace negotiations with Israel.
Al Jazeera has gained exclusive access to the content of letters that Mahmoud Abbas, the Palestinian president, despatched with Erekat, in which he accuses Israel of exploiting Palestinian and Arab goodwill.
Abbas says Israel's stepped-up settlement activity, especially in East Jerusalem, threatens to "permanently derail peace talks".
In the letter, he also calls on the Quartet to take "effective" steps against Israel.