The clashes, not only coinciding with Ramadan, but also with the Christian and Jewish festivals of Easter and Passover respectively, come at a tense period in Israel and the Palestinian territories.
In recent weeks, there has been a spate of terrorist attacks by Palestinians targeting Israeli cities, including a deadly shooting in Tel Aviv which saw three people killed. In response, Israeli forces have stepped up raids and arrests in the occupied West Bank.
Since March, Israeli forces have killed 29 Palestinians as in the course of carrying out raids in the West Bank after Palestinian assailants killed 14 Israelis in a string of attacks in Israeli cities.
But Jerusalem is particularly sensitive.
Israel claims all of Jerusalem as its eternal, indivisible capital. Palestinians seek to make East Jerusalem, including its Muslim, Christian and Jewish holy sites, the capital of a future state.
Last year saw nightly clashes in the city between Palestinians and Israeli police during the Muslim fasting month. Threats of Palestinian displacement in East Jerusalem and police raids at Al-Aqsa helped ignite an 11-day Israel-Gaza war that killed more than 250 Palestinians in Gaza and 13 people in Israel.
In response to the morning’s violence, Hamas said the Palestinian people had a right “to defend and protect the blessed Al-Aqsa Mosque at all costs.”
“There is no place for invaders and occupiers on our holy Jerusalem and land, and we will win the struggle of will and identity no matter how long it takes,” the Islamic militant group said.
By lunchtime, the area had been cleared and the mosque had reopened for prayers.