STORY: No serious injuries were immediately reported, and the confrontations appeared to be more limited than violence seen at the compound over the past week.
In a statement, Israeli police said dozens of Palestinians, some of them masked, had holed up in the mosque in the early morning and thrown rocks and fireworks at officers.
Violence at the compound has surged over the past week, raising global concerns about a slide back into a wider Israeli-Palestinian conflict, as the Muslim holy month of Ramadan coincides with Passover and Christianity's Easter.
Israel bars Jewish visitors from praying at the flashpoint site in Jerusalem's walled Old City or approaching Al Aqsa, Islam's third holiest site. Palestinians see such visits as a provocation.
Earlier on Thursday, Israel carried out air strikes in the Gaza Strip after a rocket launched from the Palestinian territory landed in Israel, Hamas officials and Israeli military sources said.