There has been continued violence between Palestinians and Israeli police in East Jerusalem as a deadline approached that could sink the Middle East peace talks.
The clashes began after a Palestinian man was shot dead by a private Israeli security guard on Wednesday.
Fearing more violence after Friday prayers, police blocked access to the esplanade around the al-Aqsa mosque, denying entry to all Muslim men under the age of 50.
It is the third most sacred site in Islam, but the area also includes Temple Mount, the holiest site in Judaism.
Only a small fraction of the usual number of Muslim worshippers were allowed through. Many others prayed as near as possible to the mosque.
The already high tensions were cranked up further when an Israeli warship fired on a Palestinian fishing boat off the Gaza Strip, killing one ban on board.
A Israeli military spokesman said the vessel had gone beyond a line set by Israel to prevent arms smuggling.
Palestinians say the fishing zone is too small to provide for those living on the Gaza Strip.