Police said masked Palestinian youths at the mosque threw stones at security forces while protesters held aloft photographs of the 18-month-old child killed in Friday's arson attack in the occupied West Bank, according to a report by AFP on Sunday.
Israeli media reported that security forces later sought to create a barrier between the stone-throwers and tourists visiting the mosque complex.
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 the army said was shot by soldiers after hurling a Molotov cocktail.
Clashes had also rocked Al-Aqsa a week ago when Palestinians were angered over Jews' access to the compound on an annual day of Jewish mourning. Visits are allowed to the complex, but Jewish prayer is prohibited.
Israeli police briefly entered the mosque during those clashes to shut the doors and lock rioters inside.
Israel seized east Jerusalem, where Al-Aqsa is located, in the Six-Day War of 1967 and later annexed it in a move never recognized by the international community.