Israeli police added extra security and imposed age restrictions on worshipers allowed into the holy site, but midday prayer on Friday -- often the flashpoint for clashes -- passed in relative calm.
Women of all ages were permitted to pray at the site, which Muslims call the Noble Sanctuary and is known to Jews as the Temple Mount, but only men over the age of 50 were allowed in.
Younger worshipers gathered outside Israeli police barricades, praying in the midday sun. When prayers ended shortly after noon, the majority of the group left quickly and peacefully.
A small group of worshipers stayed behind, holding a nonviolent demonstration, facing a line of Israeli police.
The demonstration continued for hours, with chants of "Allahu Akbar" -- Allah is the greatest -- but eventually both groups of police and demonstrators dwindled. The Palestinian Red Crescent reported four people were injured.
The decision to impose age restrictions came in the aftermath of clashes between Muslim worshipers and Israeli security forces Thursday, the latest unrest to emerge since two police officers were killed
close to the entrance of the holy site on July 14.
Israeli authorities labeled the shootings as a terrorist attack. Three Arab men from northern Israel were shot and killed by police while carrying out the attack.
Israeli authorities responded by installing security cameras and metal detectors. The decision to install the measures, seen as a unilateral step by Israel, angered the Muslim community in Jerusalem and the region.
Following days of deliberations, Israel removed the extra security measures.
The move was supposed to defuse the tension in Jerusalem and quiet a growing diplomatic rift with Jordan, which has custodianship of the holy site.
But any hopes of quelling the growing tension with Jordan were soon dashed. On Thursday, Jordan's King Abdullah II slammed Israeli Prime Minister Benjamin Netanyahu, tweeting that the Prime Minister's conduct "angers us all, threatens regional security & fuels extremism."
Tensions in the streets
Tensions in the streets of Jerusalem remain high, with occasional confrontations between Muslim worshipers and Israeli police erupting Thursday, when worshipers agreed to enter the site for the first time in two weeks after the removal of the security measures. But delays in opening at least one of the gates to the al-Aqsa compound devolved into occasional clashes.
Israeli police threw stun and smoke grenades, while some protesters threw stones and plastic water bottles.
Israeli police arrested dozens of Palestinian protesters Thursday night who had barricaded themselves inside the al-Aqsa mosque and refused calls to leave from both police and Islamic Waqf, the Jordanian authority in charge of managing the site, police spokeswoman Luba Samri said.
Before the age restrictions were announced, authorities said they expected more clashes Friday, as Muslims leaders in Jerusalem asked mosques to close for Friday prayer so that worshipers go to al-Aqsa.
For Palestinians, the removal of the security measures is seen as a measure of victory. Israel's decision to take down the metal detectors and security cameras is largely viewed as a capitulation, both by Israelis and Palestinians.
In a separate development Friday, a Palestinian stabbing suspect was shot and killed in Gush Etzion in the southern West Bank when he attempted to attack soldiers at the scene, according to a statement from the Israeli military.
The Palestinian Ministry of Health identified the suspect as 24-year-old Abdullah Ali Taqatqah from Beit Fajar in the southern West Bank.
Similar "lone wolf" attacks have happened infrequently in the last year. It was unclear Friday to what extent, if any, the incident was connected to tensions and protests surrounding the Old City of Jerusalem over the last two weeks.
Meanwhile, clashes, largely routine, erupted in other places in Jerusalem and the West Bank, including Qalandiya, Bethlehem, and Hebron. The Red Crescent said 50 people were injured.