It is the third holiest site for Muslims and allowing Jews to pray there threatens to exacerbate tensions in the occupied territory.
An Israeli judge's conclusion this week that "quiet" Jewish prayer should be allowed at the Al Aqsa mosque compound, revered by Muslims and Jews, has stirred Palestinian anger over the Jerusalem flashpoint.
Al Aqsa is at the heart of the Israeli-Palestinian conflict, falling within Israeli-annexed east Jerusalem, but administered by the Waqf Islamic affairs council.
It is the third holiest site in Islam.
The Waqf called the Tuesday ruling by Jerusalem Magistrates' Court judge Billha Yahalom an illegitimate "provocation," while Palestinian prime minister Mohammed Shtayyeh warned Israel against any moves to enforce it.
Turkey condemned the decision.
Even Israeli police have appealed the decision, which came in response to a petition by an Israeli rabbi, Aryeh Lippo, who on September 29 was slapped with a two-week ban from the plaza after praying there.
The Waqf reluctantly grants Jews limited access to the site at certain hours, but the Jewish presence at the Al Aqsa has long been a rallying cry across the Muslim world.
Before Israel's 1948 creation, riots during the British mandate of Palestine in 1929 were linked to the possibility of Jewish prayer there.
In May this year, clashes over possible evictions in a nearby Palestinian neighbourhood spread to the mosque compound, sparking an Israeli crackdown that escalated into an 11-day war between Israel and Palestinian militants in the Gaza Strip.
No Israeli law prohibits Jewish prayer at the site, which the Jews refer to as the Temple Mount, referencing two temples that were said to have stood there in antiquity.
But since 1967, the year Israel occupied east Jerusalem including the Old City in the Six Day War, Israeli authorities have enforced a ban on Jewish prayer to prevent tensions.
Judge Yahalom's legal ruling was narrowly focused on overturning Lippo's ban from the plaza.
But commenting on his conduct, she wrote: "The appellant stood in the corner with a friend or two, there was no crowd around him, his prayer was quiet, whispered."
"I have not found that the religious acts carried out by the appellant were externalised and visible," she ruled, determining that such prayer did "not violate police instructions," and cancelling his ban from the site.
In appealing the ruling, police said Lippo engaged in "improper conduct in the public sphere."
Mainstream rabbinical authorities oppose Jewish prayer on the Temple Mount, with Jewish worship centred at the Western Wall plaza below.
In a ruling earlier this year on a petition demanding Temple Mount prayer rights for Jews, Israel's Supreme Court found that, "every Jew has the right to pray on the Temple Mount, as part of the freedom of religion and expression."
"At the same time, these rights are not absolute, and can be limited to take into account the public interest."
Muslim leaders reacted to the Jerusalem court ruling with unanimous condemnation.
"These prayers constitute provocations and a violation of the sanctity of Al Aqsa," mosque director Sheikh Omar al-Kiswani told AFP.
"This decision also has no legitimacy because we do not recognise Israeli law on Al Aqsa," he said.
The Saudi Arabia-based Organisation of Islamic Cooperation strongly condemned "the decision of the so-called Israeli Jerusalem Court.'"
An open war
Palestine's Minister of Jerusalem Affairs Fadi Al-Hadmi said Palestinians in occupied East Jerusalem are "facing an open war at all aspects of life" launched by Israel.
"No one single day passes without an Israeli decision or violation against the city and its residents, the last was a decision by an Israeli court to allow Jewish extremist groups to perform religious rituals inside Al Aqsa Mosque complex," Al-Hadmi said in a statement.
Al-Hadmi called on Arab and Islamic countries to stand against Israeli assaults and violations against Jerusalem and Al Aqsa Mosque.
Turkey reacts strongly
Foreign Ministry of Turkey "strongly" condemned the decision of the judge that "has a potential to erode the status quo."
In a statement, Turkey invited the international community to stand against this "wrong, illegitimate, and dangerous decision and all other provocations."