Palestinian youths at the mosque threw stones at Israeli forces while protesters held aloft photographs of the 18-month-old child killed in Friday's arson attack in the occupied West Bank.
Calm began to return to the hilltop complex in Jerusalem's Old City later in the morning, an AFP photographer reported.
A wave of protests has swept the Palestinian territories since Friday's firebombing, which also critically wounded the toddler's four-year-old brother and parents.
On Saturday, clashes broke out at Jalazon refugee camp in the West Bank, where the funeral took place for Laith Khaldi, 16, who was shot by the Zionist army soldiers.
Clashes had also rocked Al-Aqsa a week ago when Palestinians were angered over settlers’ access to the compound.
Israel occupied east Jerusalem, where Al-Aqsa is located, in the Six-Day War of 1967.