The planned visit by a Jewish group including ultra-nationalist politicians was to have taken place a week after the attempted assassination of one of its leading activists by a Palestinian gunman prompted Israel to close the site, which is holy to both Jews and Muslims.
"Dozens of masked protesters threw stones and firecrackers at security forces who then entered the Temple Mount and pushed the demonstrators inside the (Al-Aqsa) mosque," police spokeswoman Luba Samri said, using the Hebrew term for the compound.
The clashes erupted with protesters hurling stones and firecrackers after police opened the Mughrabi Gate to visitors.
The gate, which lies at the southwestern corner of the plaza, is the only entrance to the compound for non-Muslims.
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Police then entered the plaza and the protesters fled inside the mosque, where they had set up obstacles to prevent anyone from shutting the doors and locking them inside -- a regular occurrence when clashes erupt at the site.
The compound was then reopened to visitors, although the protesters remained locked inside the mosque, she added.
The clashes quickly spread into the alleys of the surrounding Old City, an AFP correspondent reported.
Near Lions' Gate, one of the seven entrances to the walled Old City, Israeli police fired tear gas and percussion grenades to disperse a large crowd of angry Palestinians.
The clashes took place as tensions soared over demands by Jewish hardliners to be able to pray inside the mosque compound and the expansion of Israeli settlement activity in annexed Arab east Jerusalem.