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An eyewitness video reportedly taken at al-Aqsa Mosque on Friday.
The images are intended to show Israeli security forces entering the mosque and using tear gas and stun grenades.
Thousands of Palestinians had gathered in and around the mosque for prayer during the Muslim month of fasting, Ramadan.
The police initially denied that they had entered the mosque, but only on the premises.
According to the Palestinian Red Crescent, more than 150 Palestinians were injured in the clashes with Israeli security forces, mainly through the use of tear gas and rubber bullets.
Three Israeli police officers were also injured, and hundreds of Palestinians were arrested, police said.
The reason for the operation was a large group of young Palestinians who threw firecrackers and stones towards the Jewish place of worship at the Western Wall around 4 a.m.
The police had entered the area to break up the crowd and prevent further violence.
The director of al-Aqsa Mosque, Omar al-Kiswani, said that an Israeli "attack inside al-Aqsa Mosque" also took place and condemned it.
According to the AP news agency, the Israeli police later entered the mosque and arrested several people.
Israeli security forces entering the mosque rarely happen and are usually immediately seen as a provocation.
The Temple Mount is the holiest site for Jews - on the same hill stands the al-Aqsa Mosque, the third holiest site for Muslims.
This year in Jerusalem, three major religious festivals fall on the same weekend: Muslim Ramadan, Jewish Passover and Christian Easter.
Tens of thousands of tourists and pilgrims are expected in the city.
The security situation in Israel and the Palestinian territories is extremely tense: 14 people have been killed in four attacks in Israel in the past few weeks.
Israeli forces killed more than 20 Palestinians in operations in the West Bank.
After the clashes in the morning, the mosque reopened to worshipers at noon.
