Members of Israeli security forces deploy as Palestinians demonstrate against the establishment of Israeli outposts on their lands, in Beit Dajan east of Nablus in the occupied West Bank, on April 29, 2022. AFP
The Palestinian Red Crescent, which gave the toll, said no one was seriously hurt but 22 people were taken to hospital.
Israeli police released footage that showed young men on the compound hurling stones and fireworks in Friday's early hours. Officers entered the site at dawn.
A police statement said they went in to contain "rioters and lawbreakers" some of whom were trying to throw stones down towards the Western Wall, the sacred Jewish site below Al-Aqsa.
Police said officers used "riot dispersal means" to contain the unrest and that two people had been arrested, one for throwing stones and the other one for "inciting the mob".
An AFP journalist said Israeli police fired rubbet-coated bullets while a witness said they also used tear gas.
An uneasy calm had been restored at the compound following the unrest that surrounded morning prayers, but tensions remained high.
In the early afternoon, a crowd of Muslim worshippers gathered at Al-Aqsa. Some people waved Palestinian flags and the colours of the Gaza Strip-based Hamas militant group, an AFP journalist said.
Over the past two weeks, nearly 300 Palestinians have been hurt in clashes at Al-Aqsa, Islam's third-holiest site which is also the holiest site for Jews, who call it the Temple Mount.
The site is located in east Jerusalem, which Israel captured in the 1967 Six-Day War and later annexed, in a move not recognised by most of the international community.
Israel's incursions into the compound during Ramadan met widespread condemnation and raised fears of inflaming persistent Israeli-Palestinian tensions across Jerusalem.
But the Jewish state has insisted it has been compelled to act against operatives from Islamist groups Hamas and Islamic Jihad. It says the militants threaten Muslim worshippers at Al-Aqsa and Jews praying at the Western Wall.
In an apparent attempt to ease tensions, Israel's Foreign Minister Yair Lapid has stressed that the government is committed to the status quo at the compound, meaning adherence to the long-standing convention that only Muslims are allowed to pray there.
Jews are allowed to visit the Temple Mount.
Muslim leaders have, however, been angered by a recent uptick in such visits. Some voiced fears that Israel was seeking to divide the compound and create a space where Jews may worship. Lapid told journalists that no such plan exists.
The fresh unrest comes as the end of Ramadan nears early next week.
Violence in Israeli-annexed east Jerusalem has raised fears of another armed conflict similar to an 11-day war last year between Israel and Hamas, triggered by similar unrest at Al-Aqsa.
Since early last week, there has been isolated rocket fire from Gaza towards Israel and Israeli reprisals, but no casualties reported on either side.
Hamas held a rally in Gaza late Thursday, with calls to "defend" Jerusalem including Al-Aqsa.
In an annual show of pro-Palestinian rallies known as Quds (Jerusalem) Day, thousands of Iranians took to streets across the Islamic republic on Friday. Flag-waving protesters chanted "Death to America" and "Death to Israel", the state broadcaster IRIB reported.
The Al-Aqsa tensions have come against a backdrop of violence since March 22 in Israel and the occupied West Bank.
Twelve Israelis, including an Arab-Israeli police officer, and two Ukrainians were killed in four separate attacks inside Israel. Two of the deadly attacks were carried out in the Tel Aviv area by Palestinians.
A total of 26 Palestinians and three Israeli Arabs have died during the same period, among them perpetrators of attacks and those killed by Israeli security forces in West Bank operations.