STORY: At least 12 Palestinians were injured in the early morning clashes at Islam's third-holiest site, the Palestinian Red Crescent said.
Israeli police said they intervened when hundreds of people began hurling rocks and fireworks, including in the direction of the Western Wall, where Jewish worshippers gather.
There were almost daily confrontations at the mosque this month when Ramadan overlapped with the Jewish celebration of Passover, which brought hundreds of thousands of Muslims and Jews to the heavily policed compound in the old city.
However, the violence had abated this week following the end of Passover and after Israel halted Jewish visits to the huge esplanade, home to the Dome of the Rock and the Al-Aqsa mosque.
Israeli officials have blamed tensions this month on Islamist groups, including Hamas, which rules the Palestinian enclave Gaza, saying they have encouraged youths to stage riots aimed at stirring anger in the Muslim world against Israel.
Palestinians accused Israel of not doing enough to enforce a long-standing ban on Jewish prayer on the esplanade. Israel rejects this accusation.