An AFP correspondent witnessed the clashes break out shortly after the worshippers entered.
The Palestinian Red Crescent reported 56 people wounded both inside the Haram al-Sharif compound, known to Jews as the Temple Mount, and in the immediate area.
Outside, clashes in one area erupted when a group of policemen walked in the middle of a crowd. Palestinians threw plastic bottles and Israeli forces fired stun grenades.
Israeli police said stones were thrown at officers inside the compound.
"Upon the entry of worshippers into the Temple Mount compound, some began throwing stones at officers, during which some stones fell into the Western Wall plaza," Israeli police said in a statement, referring to the Jewish holy site below the compound.
"A police force at the site pushed back those disrupting the orders using riot dispersal means. An officer was hit by a stone on his head. He was treated at the site."
Thousands of worshippers had earlier streamed into the compound for afternoon prayers for the first time in two weeks, ending a boycott after Israel removed controversial new security measures, installed after a July 14 attack killed two policemen.
The site includes the Al-Aqsa mosque and the Dome of the Rock.
Some cried as they entered while others shouted "Allahu Akbar" (God is Greatest). Some brought their children in what was initially a celebratory atmosphere.
Muslims had in previous days refused to enter the compound and prayed in the streets outside after Israel installed the new security measures.
Palestinians viewed the move as Israel asserting further control over the site.
Israeli authorities said the measures, including metal detectors, were needed because the July 14 attackers smuggled guns into the compound and emerged from it to attack the officers.
Warnings Over Friday Prayers
Deadly unrest erupted in the days after the new measures were introduced, with clashes breaking out around the compound and in the occupied West Bank, leaving five Palestinians dead.
A Palestinian also broke into a home in a Jewish settlement in the West Bank last week and stabbed four Israelis, killing three of them.
There had been concerns that Friday's main weekly Muslim prayers -- which typically draw thousands to Al-Aqsa -- would lead to serious clashes between protesters and Israeli security forces if a resolution was not found.
After intensive international diplomacy, Israel removed the metal detectors on Tuesday.
Newly installed railings and scaffolding where cameras were previously mounted were also removed early on Thursday.
Police said on Thursday morning that all new security measures had been taken away.
The removal was seen as a defeat for Israeli Prime Minister Benjamin Netanyahu, who had ordered the new security measures and was forced to backtrack after warnings the unrest could spiral out of control.
It represented a rare victory for Palestinians, who remained united in their boycott.
In the pre-dawn hours of Thursday, crowds of Palestinians gathered at the entrance of the site to celebrate, with whistling and constant horns from cars.
Young men set off firecrackers as Israeli forces watched closely.
Firas Abasi said he felt like crying over the "victory".
"For 12 days no one has slept, no one has done anything except the Al-Aqsa mosque," he said.
Israeli officials had said they were to replace the new security measures with "advanced technologies" -- widely believed to be smart cameras with facial recognition technology.
It was not immediately clear if Israel would stick to reported plans to install the smart camera system in Jerusalem's Old City. Cameras are already widespread inside its walls.
Jordan is the custodian of Muslim holy sites at the compound, and King Abdullah II had called on Netanyahu to remove the security measures.
Information Minister Mohammad al-Momani on Thursday welcomed their removal, calling it an "essential step towards calm."
However, Abdullah on Thursday also called for an Israeli security guard at Israel's embassy in Amman to face trial over an incident on Sunday, threatening a fresh crisis in relations.
The guard shot dead a 17-year-old Jordanian who attacked him with a screwdriver, according to Israeli officials. Another Jordanian was also killed, apparently by accident.
The guard was allowed to return to Israel on Monday after a deal said to involve the holy site, but Netanyahu's embrace of the guard as a hero angered Jordanian officials.
The holy compound lies in east Jerusalem, seized by Israel in the Six-Day War of 1967 and later annexed in a move never recognised by the international community.
The third-holiest site for Muslims and the most sacred for Jews, it is at the heart of the Israeli-Palestinian conflict and has served as a rallying cry for Palestinians.
In 2000, a visit to the compound by then Israeli opposition leader Ariel Sharon helped ignite the second Palestinian intifada, or uprising.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)