By recalling its ambassador to Israel, the Hashemite kingdom sent a message that deploying police inside the mosque compound had crossed a red line and put their diplomatic ties in jeopardy.
In parallel, Jordan's King Abdullah II hosted a diplomatic push which brought together US Secretary of State John Kerry and Israeli Prime Minister Benjamin Netanyahu for talks in Amman on Thursday.
"Recalling the Jordanian ambassador and the diplomatic push sent a tough message to Israel that violating Al-Aqsa would endanger the peace treaty," Oraib Rantawi, head of Amman's Al-Quds Centre for Political Studies, told AFP.
The status of Jerusalem is one of the most contentious issues in the Israeli-Palestinian conflict, and the Al-Aqsa compound is the scene of frequent confrontations between protesters and police.
Also Read
Tensions soared to a new level earlier this month when Israeli police entered several yards inside the mosque during clashes triggered by a vow by Jewish far-right groups to visit the holy site.
"The violations at Al-Aqsa undermine the credibility and legitimacy of the Jordanian leadership and its ability to carry out its custodianship of the mosque," said Rantawi.
Jordan, which has a 1994 peace treaty with Israel, is home to more than two million Palestinian refugees, as well as large numbers of Jordanians of Palestinian origin.
The Al-Aqsa compound, holy to both Muslims and Jews, is one of the most sensitive spots in the Middle East.
Israel captured Jerusalem's mostly Arab eastern sector from Jordan in the 1967 Six-Day War and later annexed it in a move never recognised internationally.
In March 2013, Palestinian president Mahmud Abbas signed a deal with King Abdullah, entrusting him with the defence of Muslim holy sites in Jerusalem.
"For Jordan, Al-Aqsa is an internal issue," said Mohammad Abu Rumman, researcher at the University of Jordan's Center for Strategic Studies, pointing to its custodianship and the Palestinian origins of many Jordanians.