The far-right activists chanted racist slogans at the site, considered to be the third holiest in Islam, amid a heavy Israeli security presence.
The attacks come as Israeli forces prevented Directorate of the Reconstruction of the Blessed Al-Aqsa Mosque employees from hanging signs around the mosque to mark the holy month of Ramadan, which is due to start on Sunday.
Israeli forces have set checkpoints at the Wadi Al-Rababa junction in the town of Silwan, which is located south of Al-Aqsa Mosque, and searched cars and checked people's IDs.
The deputy head of Hamas’ political bureau, Saleh Al-Aouri, told Israel not to use violence or provocations against Palestinians at Al-Aqsa and Jerusalem during Ramadan, in a televised interview on Monday.
He also warned of "comprehensive confrontation" if Israeli forces - who occupy the West Bank and East Jerusalem - "persist in their aggression".
"The next confrontation with the occupation will be of a broader popular and official scope, and will constitute a turning point in the history of the conflict," he added.
Israel launched a brutal crackdown on peaceful protests and prayer gatherings in Jerusalem last Ramadan, including Al-Aqsa Mosque resulting in Hamas firing rockets into Israel.
An Israeli bombardment of Gaza - which Hamas runs - led to 250 Palestinians being killed including dozens of children.
Israel invaded the West Bank in 1967, and has occupied it ever since. Palestinians in Jerusalem and the West Bank are often at the receiving end of intimidation and violence from Israeli forces and Jewish settlers.
Palestinians are routinely banned from entering Al-Aqsa Mosque, while far-right Israeli activists and settlers are also allowed to march and attack Palestinians, often without consequences.