Israel has deployed more than 1,300 police across occupied East Jerusalem to prevent violence after days of clashes at the Al-Aqsa mosque compound.
Al Jazeera's Imtiaz Tyab, reporting from the Old City, said there was a "huge security presence" around Al-Aqsa before noon prayers on Friday.
Police were then deployed to flashpoint neighbourhoods where Palestinian stone-throwers and security forces clashed later in the day.
For weeks, there have been near-daily scuffles in East Jerusalem, triggered by fears that Israel was preparing to change the rules about who can worship at the Al-Aqsa compound, which is holy to Jews as well as Muslims.
Police barred men of 35 and under from attending Friday prayers. Riot police manned metal barricades, checking identity papers and directing pedestrians.
At one checkpoint in the Wadi Joz area, just outside the Old City, about 500 young Palestinians who were denied entry to the mosque compound because of their age performed prayers on a street. They were faced by a row of riot police in black uniforms and helmets, as well as several officers on horseback.
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About 15,000 people gathered to pray at Al-Aqsa and the event ended peacefully, but clashes erupted in other parts of East Jerusalem and in the occupied West Bank.
At the Qalandia checkpoint separating Ramallah from Jerusalem, troops fired rubber bullets as several hundred protesters marched, some throwing rocks and petrol bombs, according to the Reuters news agency.
In East Jerusalem, police fired tear gas to disperse protesters hurling firecrackers and burning tyres that sent up huge clouds of black smoke in Shoafat refugee camp.
Israeli Prime Minister Benjamin Netanyahu spoke by phone with Jordan's King Abdullah II on Thursday to reassure him that the government would not yield to increasing demands by Jewish hardliners to allow Jews to pray at Al-Aqsa.
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Jordan acts as the custodian of the Al-Aqsa mosque compound and other Muslim holy sites in annexed East Jerusalem.
The Al-Aqsa complex is known to Muslims as Haram as-Sharif, or Noble Sanctuary, and to Jews as the Temple Mount.
It is the third holiest site in Islam and houses the Al-Aqsa Mosque and the gold-topped Dome of the Rock. Jews also revere it as the location of their biblical temples and consider it the most sacred location in their faith.
In recent months, several senior members of Netanyahu's coalition, including Housing Minister Uri Ariel and Deputy Parliament Speaker Moshe Feiglin, have called for a greater Jewish presence and the right to pray on the mount.
At the same time, the number of Jewish visitors to the site has increased over the years, raising fears among Muslims that this is part of a gradual Jewish takeover.
Tension escalated further on Wednesday after Israeli security forces stormed the Al-Aqsa Mosque.
The Islamic Waqf, the Jordanian religious trust that administers Al-Aqsa, said two people were injured inside, and that Israeli security forces used foam-tipped bullets, stun grenades and tear gas against protesters.
Israeli security forces also damaged the mosque's doors, burnt carpets and broke glass during the confrontation, the Waqf said.
Later on Wednesday, a Palestinian man rammed his car into two groups of pedestrians. A second Israeli died on Friday from injuries sustained in the attack, after a border police officer was killed at the scene.
It was the second such deadly attack by a Palestinian driving a car in two weeks. In both cases, the perpetrators were shot dead by police.
The EU's new foreign affairs chief said the upsurge in violence made it all the more critical that Israel and the Palestinians resume talks.
"The risk of growing tensions here in Jerusalem ... is that, if we do not move forward on the political track, we will go back, and back again to violence," Federica Mogherini told reporters on Friday after meeting Israeli Foreign Minister Avigdor Lieberman during her first official visit to the region.
The last talks between Israel and the Palestinians broke down in April after months of largely fruitless negotiations.
Source: Al Jazeera and agencies