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The meeting came as another Israeli was wounded in a new knife attack west of Jerusalem, the latest in a spate of unrest that erupted on October 1 and has sparked fears of a new Palestinian intifada, or uprising.
UNESCO faults Israeli handling of holy sites
UN chief Ban Ki-moon had said on Wednesday after talks with both sides that he was "not optimistic", as he appealed for calm after three weeks of deadly unrest.
"Our most urgent challenge is to stop the current wave of violence and avoid any further loss of life," said Ban, who is due to meet Jordan's King Abdullah II on Thursday.
Kerry, who will also hold talks with Palestinian president Mahmud Abbas at the end of the week, "feels it's important to go and to have these discussions, given the on-going violence, to try to look for ways to end that violence and to restore calm," his spokesman John Kirby said.
"As well as to provide some political breathing space, so that real, meaningful progress can be made towards — towards an end to the violence."
German Foreign Minister Frank-Walter Steinmeier will also host Kerry and Netanyahu separately for talks in Berlin.
The EU's top diplomat Federica Mogherini is also in the German capital to meet the Israeli premier Thursday, before holding talks with Abbas "in the coming days".
Netanyahu has so far shown little appetite for compromise. When meeting Ban on Tuesday, he harshly criticised Abbas for "fanning the flames" and rejected allegations that Israel has used excessive force.
He repeated the assertion in Berlin on Wednesday, laying the blame on Abbas. "If we want to have peace we have to stop terror. And to stop terror we have to stop incitement," he said after talks with Chancellor Angela Merkel.
In the latest case of violence, an Israeli was wounded in a new knife attack west of Jerusalem on Thursday before police shot and "neutralised" the two assailants, police said.
The male attackers had attempted to board a bus in Beit Shemesh but were prevented from doing so by passengers. They then stabbed a 25-year-old Jewish passer-by close to the bus station before being fired on by officers.
The police did not specify whether the attackers were killed or wounded. The attack is the latest in a series of stabbings — mostly by young Palestinians — against soldiers, police or Israeli civilians.
Since October 1, at least 49 Palestinians and one Israeli Arab have been killed, including alleged attackers. Eight Israelis have been killed in attacks.
UN chief to brief Security Council on Israeli-Palestinian violence
In his behind-closed-doors report to the Security Council Wednesday, Ban delivered a sobering assessment of prospects for a return to calm, according to a diplomat, saying there was no time to waste to press for a de-escalation and pull the sides back from the brink.
The UN chief presented a report prepared by his legal experts on international protection after the Palestinians called for the deployment of an observer force in east Jerusalem.
The report, seen by AFP, outlines 17 cases — from Trieste after World War II to Kosovo in 1999 — when the Security Council stepped in and set up special regimes to guarantee the protection of civilians.
In a letter to the council, Ban said the report should not be seen as an "options paper" for addressing the crisis but added that it could be useful in "informing future work on this subject".
Abbas meanwhile called on Israel to strictly respect rules governing Israeli-annexed east Jerusalem's flashpoint Al-Aqsa mosque compound, known to Jews as the Temple Mount.
Clashes between Israeli security forces and Palestinian protesters at the compound in September sparked the current wave of violence.
Violent protests have also erupted in east Jerusalem, the occupied West Bank and the Gaza Strip.
"The continued occupation and aggression against Christian and Muslim holy sites in east Jerusalem, particularly against Al-Aqsa, opens the door to a religious conflict, which has unfortunately started," said Abbas.
Netanyahu has repeatedly accused Abbas of incitement by suggesting Israel wants to change the status quo of the compound, sacred to both Muslims and Jews.
Muslims fear Israel will seek to change rules governing the site, where Jews are allowed to visit but not pray to avoid provoking tensions. Netanyahu says he has no intention of changing the rules.
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