While thousands of Muslims prayed without incident at the ultra-sensitive site, young Palestinians clashed with Israeli police in the occupied West Bank and Gaza strip, leaving scores injured by Israeli gunfire, according to emergency services.
The international community has scrambled to defuse a wave of violence that many fear heralds a third Palestinian intifada, or uprising, and UN Secretary-General Ban Ki-moon said it was time for Israeli and Palestinian leaders to meet face to face.
Ban's appeal came as tensions showed little sign of easing, with Palestinian movements holding a "day of rage" today against Israel.
Angry youths lobbed stones at Israeli police who responded with tear gas and gunfire at numerous checkpoints in the occupied West Bank, where 20 Palestinians received gunshot wounds.
According to emergency services, 65 people, including three journalists, were hit by Israeli fire in the blockaded Gaza Strip.
Meanwhile the Israeli army said an Israeli woman and her two daughters were injured in the West Bank when her car was hit with a Molotov cocktail.
Sheikh Azzam al-Khatib, head of the Islamic Waqf which administers Al-Aqsa, said 25,000 Muslims attended today prayers after age restrictions were lifted for the first time since mid-September, when clashes broke out at the site between Palestinians and Israeli police.
Israeli police estimated the crowd today at 30,000.
"Of course it is better but there are still checkpoints and searches. There is still no respect," said worshipper Wissam Abu Madi, 20, who said he believed a wave of attacks on Israelis would continue.
Clashes erupted during Jewish religious holidays last month as an increase in visits by Jews to the compound raised fears among Muslims that Israel was planning to change longstanding rules governing the site.
To avoid tensions Jews are allowed to visit but not pray at the site located in east Jerusalem, which was annexed by Israel in 1967.
It is managed by the Jordanian-run Waqf but Israel controls access.
The protests at Al-Aqsa triggered a wave of lone-wolf knife attacks, shootings and car-rammings against Israelis.
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