Israeli security forces used tear gas as they clashed with Palestinian “stone throwers” at the al-Aqsa mosque in East Jerusalem.
Police said they closed the doors to lock in rioters throwing stones, fireworks and other objects, according to the BBC.
The conflict later continued outside the mosque complex, as the police fired tear gas and stun grenades.
The incident occurred just hours before the start of the Jewish New Year, Rosh Hashanah, which begins on Sunday evening and lasts until Tuesday evening.
Al-Aqsa Mosque is considered one of Islam’s holiest sites, and is also in the Temple Mount site revered by Jews.
It has been a source of religious and political tension between Israel and the Palestinians, and a frequent flashpoint for violence.
Last week, Israeli Defence Minister Moshe Ya'alon outlawed two Muslim groups that confront Jewish visitors to the compound. He said the ban was necessary to "defend the security of the state, the well-being of the public and public order".
According to police, rioters barricaded themselves in the mosque overnight with the aim of disrupting Jewish visits to the site ahead of the start of the New Year celebrations on Sunday evening.
"Masked protesters who were inside the mosque threw stones and fireworks at police," a police statement said. "Suspect pipes that could be filled with homemade explosives were also found at the entry to the mosque."
While non-Muslims are allowed to visit the compound, Jews are forbidden from praying or displaying national symbols, for fear of triggering tensions with Muslim worshippers.
Israel seized east Jerusalem, where the mosque is located, in the Six Day War of 1967 and later annexed it. The move was never recognised by the international community.
Last week, Press TV reported that Israeli soldiers and police officers prevented more than 40 Palestinian women from entering the al-Aqsa Mosque.
When Israeli forces tried to detain one of the women, the Palestinian worshippers repelled the attack.Reuse content