Friday's violence -- a stabbing attack that killed three Israelis and clashes which left three Palestinians dead -- was among the most severe in recent years.
There were concerns over whether it would spark wider unrest as Israeli officials grappled with how to ease tensions over the Haram al-Sharif mosque compound, known to Jews as the Temple Mount.
The site in Jerusalem's Old City that includes the revered Al-Aqsa mosque and Dome of the Rock has been a rallying cry for Palestinians.
In 2000, then Israeli opposition leader Ariel Sharon's visit to the compound helped ignite the second Palestinian intifada, or uprising, which lasted more than four years.
Tensions have risen throughout the past week because of new Israeli security measures at the compound following an attack nearby that killed two policemen on July 14.
The measures have included the installation of metal detectors at entrances to the site, which Palestinians reject since they view the move as Israel asserting further control over it.
Israeli authorities say the July 14 attackers smuggled guns into the holy site and emerged from it to shoot the policemen.
Friday's main weekly Muslim prayers -- which typically draw thousands to Al-Aqsa -- brought the situation to a boil.
In anticipation of protests, Israel barred men under 50 from entering the Old City for prayers, stoking further Palestinian anger.
Clashes broke out between Israeli security forces and Palestinians around the Old City, in other parts of annexed east Jerusalem and in the occupied West Bank.
- Abbas freezes contacts -
Three Palestinians between the ages of 17 and 20 were shot dead. The Palestinian Red Crescent reported 450 people wounded in Jerusalem and the West Bank, including 170 from live or rubber bullets.
In the evening, a Palestinian broke into a home in a Jewish settlement in the West Bank during a Sabbath dinner and stabbed four Israelis, killing three of them.
The 19-year-old Palestinian was shot by a neighbour, an off-duty soldier, and was taken to hospital.
The Israeli army said he had spoken of the Jerusalem holy site and of dying as a martyr in a Facebook post.
The Israelis killed in Neve Tsuf, north of Ramallah and also known as Halamish, were a grandfather and two of his children, an Israeli military official said. The grandmother was wounded.
Israeli soldiers raided the Palestinian's nearby village of Kobar overnight and arrested his brother, an army spokeswoman said.
Preparations were also being made to demolish the attacker's home, a measure Israel regularly employs because it views it as a deterrent, although human rights groups say it amounts to collective punishment.
Amid mounting pressure to respond to the dispute over the mosque compound, Palestinian president Mahmud Abbas announced late Friday he was freezing contacts with Israel.
There was no immediate public reaction from Israeli Prime Minister Benjamin Netanyahu.
- 'For all Muslims' -
"Violence is likely to worsen absent a major policy shift," said Ofer Zalzberg, a senior analyst at the International Crisis Group.
"Netanyahu's mistake was installing the metal detectors without a Muslim interlocutor. It is the coercive character more than the security measure itself that made this unacceptable for Palestinians."
On Saturday, entrances to Jerusalem's walled Old City were open, but heavy security was in place.
The metal detectors also remained at the entrance to the mosque compound.
"Al Aqsa –- that's for the Muslims, not for the Jewish," said Mohammad Haroub, a 42-year-old souvenir shop owner.
Like hundreds of others, he prayed outside on Friday instead of passing through the metal detectors.
He added that it was not only an Israeli-Palestinian issue.
"Al Aqsa is not for Palestinians. It is for all Muslims."
Sharon Kopel, a 46-year-old Israeli tour guide leading a group in the Old City, said he felt the metal detectors were unnecessary and politically motivated, but also criticised Palestinians for "lies" about Israel trying to take over Al-Aqsa.
"I don’t think it’s really effective anyway," he said of the new security measures. "But on the other hand... they brought guns into a holy place."
The Haram al-Sharif/Temple Mount is central to the Israeli-Palestinian conflict.
It lies in east Jerusalem, seized by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.
It is considered the third holiest site in Islam and the most sacred for Jews.
