Israel has sent extra troops into the occupied West Bank and its police dispersed stone-throwing Palestinians in Jerusalem as international concern mounted over the deadliest outbreak of violence between the two sides for years.
The Palestinian Health Ministry said one Palestinian was killed during a separate clash outside the city on Saturday, taking the death toll from the past two days to seven.
Three Israelis were stabbed to death on Friday in a West Bank settlement.
Hours earlier, three Palestinians were killed in violence prompted by Israel's installation of metal detectors at entry points to the Noble Sanctuary-Temple Mount compound in Jerusalem's Old City.
Russia, the US, the EU and the UN said in a joint statement they were "deeply concerned by the escalating tensions and violent clashes" and called for restraint on all sides.
Diplomats said the UN Security Council would meet to discuss how to de-escalate the situation on Monday following a request from Sweden, Egypt and France.
Palestinian President Mahmoud Abbas ordered all official contact with Israel suspended until it removed the metal detectors at the holy compound in Jerusalem, where Muslims pray at Al-Aqsa mosque.
Israel's security cabinet was to convene on Sunday and is expected to discuss alternative security measures to replace the metal detectors, according to two Israeli officials.
In Jerusalem, Israeli police used riot gear to disperse dozens of Palestinians who threw stones and bottles at them. Television footage showed police throwing stun grenades and using a water cannon to break up the crowd.
In the West Bank, Israeli forces raided the home of the Palestinian attacker who fatally stabbed the three Israelis and wounded another on Friday, the military said.
An Israeli military spokespeson said the attacker's brother was arrested and security forces were restricting movement of Palestinians from his village.
The stabbing victims were from the West Bank settlement of Neve Tsuf. The attacker, Omar Alabed, who invaded their home, was shot and taken to a hospital for treatment, the military said.
Alabed posted a note on Facebook prior to the attack, writing: "I am going there and I know I am not going to come back here, I will go to heaven. How sweet death is for the sake of God, his prophet and for Al-Aqsa mosque."
Israeli Defence Minister Avigdor Lieberman met with senior commanders in the West Bank to assess the situation and said the attacker's home would be promptly demolished, in line with Israeli policy. He called on Abbas to condemn the attack, describing it as a "slaughter".
The Palestinian Health Ministry said two Palestinians died of gunshot wounds in two neighbourhoods of East Jerusalem and it later reported a third Palestinian fatality
Israel decided to install the metal detectors at the entry point to the shrine in Jerusalem about a week ago after the killing of two Israeli policemen stationed there.