The demonstrators chanted slogans in support of the Palestinian resistance movement of Hamas and its military wing, the Ezzedine al-Qassam Brigades, on the third Friday of the holy month of Ramadan, urging the resistance forces to strike Israel.
Some 60,000 worshipers performed the Friday noon prayers at the mosque despite the Israeli restrictions in Jerusalem al-Quds.
Thousands of Palestinians from the occupied West Bank were blocked from attending the prayers at al-Aqsa.
The al-Aqsa compound had seen similar protests on Thursday night.
Over recent days, Jerusalem al-Quds has witnessed intensified tensions as Palestinians confronted acts of aggression by Israeli troops and settlers.
The tensions triggered protests in the occupied West Bank and the besieged Gaza Strip.
Separately, Israeli forces continued to attack anti-settlement protests in the occupied West Bank on Friday.
Two Palestinians were hit with rubber bullets fired by the Israeli forces at an anti-settlement protest in the village of Kafr Qaddum.
According to local sources, the Israeli troops also used tear gas against the protesters, leaving tens of them suffering from breathing difficulties.
Israeli forces attacked a similar protest in the village of Beit Dajan, east of Nablus, using live ammunition, rubber bullets, and tear gas.
The crackdown left a Palestinian injured with Israeli live fire, and three others were hit with rubber bullets, while tens of cases of breathing difficulties were reported in the village.
Israeli forces also attacked the participants in a rally staged in solidarity with the residents of the occupied West Bank village of Ein al-Bayda, which is threatened with seizure by the Israeli authorities for the benefit of the expansion of the Maon and Karmiel settlements.
Palestinian and foreign activists were among the protesters.
On Friday morning, Israeli forces shot and injured a young Palestinian man near the settlement of Efrat in the occupied West bank.
The Palestinian Information Center cited Israeli media outlets as saying that the Israeli forces opened fire on the man in al-Nashash area near the Gush Etzion bloc of settlements, south of Bethlehem, over an alleged stabbing attempt.
They said the man was hit in the head and chest and was in critical condition.
Many Palestinians have sustained injuries or lost their lives in similar incidents due to allegations that they attempted stabbing or car-ramming attacks against Israelis.
Later on Friday, local sources said clashes had erupted between Palestinians and Israeli forces after settlers set fire to Palestinian agricultural land in the village of Barqa, east of Ramallah, in the occupied West Bank.
Two Palestinians were hit with rubber bullets during the clashes.
More than 600,000 Israelis live in over 230 settlements built since the 1967 Israeli occupation of the Palestinian territories of the West Bank and East Jerusalem al-Quds.
All Israeli settlements are illegal under international law. The United Nations Security Council has condemned Israel's settlement activities in the occupied territories in several resolutions.
Palestinians want the West Bank as part of a future independent Palestinian state, with East Jerusalem al-Quds as its capital.