Al-Aqsa, in the Old City, and adjacent neighbourhoods have seen months of violence, and the mosque compound has been a rallying point for Palestinian resistance to perceived Jewish attempts to take control of it.
Jerusalem was relatively calm today a day after youths clashed with police following the shooting dead of Muataz Hijazi, a Palestinian suspected of trying to murder hardline Jewish rabbi Yehuda Glick, linked to the tensions at Al-Aqsa.
Fearing unrest after Hijazi's killing, hundreds of additional police were deployed around the Al-Aqsa mosque, restricting entry for Muslim men to those over 50.
Prayers were more sparsely attended than usual but held without incident, an AFP correspondent said.
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Azzam al-Khatib, head of the Islamic Waqf body which oversees Jerusalem's Muslim holy sites, gave a sharp sermon at Al-Aqsa, calling yesterday a "black day" and a "catastrophe".
Shortly afterwards, a handful of Palestinian youths outside the Old City threw stones at police, who quickly dispersed them, police spokeswoman Luba Samri said in a statement.
The Israelis responded with live fire and rubber bullets and wounded around a dozen people, Palestinian security sources and medics said.
Jerusalem's Old City was teeming with additional police, including many in riot gear, after an Israeli clampdown on the compound.
The closure was the first for decades and prompted a spokesman for Palestinian president Mahmud Abbas to condemn the move as an Israeli "declaration of war."
The resident imam at Abbas's headquarters in Ramallah echoed the president's words, saying the closure had been a "declaration of war ... To Muslims across the world" and calling for people to "defend" Al-Aqsa.