The clashes come as there appeared to be a lull in Israeli-Palestinian tensions over the site, which is sacred to both Muslims and Jews.
Palestinians ended a two-week-long protest of Israeli security measures after Muslim religious leaders in Jerusalem told worshippers on Thursday that they could once again enter the al-Aqsa mosque compound.
However, as thousands of worshippers returned Thursday afternoon for the first prayer at the mosque in two weeks, Palestinians clashed with police. Injuries came primarily from stun grenades and rubber bullets, the Palestinian Red Crescent said.
Clashes with police near the site - known as the Temple Mount to Jews and the Noble Sanctuary to Muslims - have led to the deaths of four Palestinians in the past week. Three Israelis were also stabbed by a Palestinian man who claimed to be defending the al-Aqsa Mosque.
The head of the Islamic Council, Abdul Atheem Salhab, said at a press conference earlier Thursday that worshippers could end their boycott of the holy site after Israel removed security installations at the entrance.
"All installations outside the gates have been removed, which is a victory to our people," Atheem Salhab said.
Israel removed the last of the security measures on Thursday, including metal railings and scaffolding, which were installed at the entrance to the al-Aqsa Mosque after a July 14 attack in which two Israeli police officers were killed. Intrusive metal detectors – the most controversial Israeli measure - had already been removed Tuesday.
Palestinians claimed that Israel was seeking to impose control over the contested site. Israel had denied such claims, saying the security installations were typical of holy sites around the world.
Palestinian President Mahmoud Abbas said he accepted the religious leaders' ruling but added that no decision had been reached on whether to restart normal relations with Israel.
Meanwhile, the Islamist Hamas movement said Thursday that the removal of security facilities at al-Aqsa was a "historic victory" but claimed that the battle for the mosque is not over yet.
Jerusalem "is Arab and Islamic land. It will remain so and will never be divided. Everyone must understand that the Palestinians will never let anyone dirty our al-Aqsa Mosque," said Hamas chief Ismail Haniyeh in an emailed statement.
Palestinians celebrated in the streets at Thursday's news, but fears remained that violence could return to the area after Friday prayers.
Israeli Prime Minister Benjamin Netanyahu was strongly criticized by right-wing politicians after the decision to remove the measures. Education Minister Naftali Bennett of the Jewish Home party told Army Radio that he believes Israel "folded" and that "Israel came out weakened from the crisis."
Palestinians react as a stun grenade explodes in a street at Jerusalem's Old city outside the Noble Sanctuary compound, after Israel removed all security measures it had installed.
At least 50 Palestinians were injured in clashes with police near the al-Aqsa mosque in Jerusalem after Muslim worshippers flocked back to the site on Thursday, Palestinian emergency medical services said.
