According to a statement from Netanyahu's office, the two leaders held a phone call to discuss "the latest incidents" at the site, which is both the third holiest place in Islam and also the most sacred site for Jews.
For several hours on Wednesday morning, heavy clashes raged at the mosque compound as Israeli police faced off with Palestinian stone-throwers bent on preventing a visit by Jewish extremists, in an incident which prompted Jordan to recall its ambassador in protest.
"Prime Minister Netanyahu reiterated Israel's commitment to preserve the status quo on the Temple Mount as well as Jordan's special status at the site," a statement from the premier's office said, using the Israeli name for the compound.
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Jordan's status as custodian of the Al-Aqsa mosque compound and other Muslim holy sites in annexed east Jerusalem is enshrined in the 1994 peace treaty between the two countries.
Under the current status quo, Jews are permitted to visit the esplanade but not to pray there for fear it would cause friction at one of the most sensitive holy sites in the Middle East.
Fears that Israel was poised to legislate changes to the status quo at the compound have stoked a wave of unrest, with young Palestinians hurling stones to prevent visits by extremist Jewish groups whose stated aim is to secure prayer rights at the site.
Israel has repeatedly insisted it has no plans to change the current status quo at the plaza, with the premier seeking to distance himself from rightwing voices within his governing coalition expressing support for such a move.
The site is revered by Jews as the location of the first and second Temple, with some fringe groups hoping to see a Third Temple built there.