His outreach came a day after Jordan, a key ally of Israel, recalled its ambassador to protest what it called an "unacceptable" Israeli police assault on the hilltop compound in Jerusalem's Old City.
Tensions were further heightened after a Palestinian slammed his van into a crowd waiting at a train stop, killing an Israeli policeman, in what his family and the militant group Hamas said was a revenge attack.
Muslims also revere it as the Noble Sanctuary, Islam's third-holiest site and home to the Al-Aqsa Mosque and the gold-topped Dome of the Rock.
Since Israel captured east Jerusalem and the Old City in 1967, Jewish worshippers have been allowed to visit but not pray at the site. The area is run by Muslim authorities under the custody of Jordan.
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It has been the focus of weeks of unrest, including clashes yesterday as a group of religious Jews planned to visit.
In the phone conversation with Jordan's King Abdullah II, Netanyahu "reiterated Israel's commitment to preserve the status quo," his office said. "Both leaders called for an immediate end to all acts of violence and incitement."
Earlier, his office said anyone calling for changes in the longstanding arrangement "is expressing a personal opinion and not the views of the government."
In Amman, the palace confirmed that Netanyahu had called. "King Abdullah stressed during the phone call Jordan's rejection for any measures harming the Al-Aqsa Mosque and its sanctity," a statement said.