Young demonstrators gathered around the mosque threw stones at police who had entered the compound in large numbers and who responded with stun grenades.
Israeli police were attempting to disperse the stone-throwers, a spokeswoman said, adding that there had been no casualties or arrests so far.
The protesters fear Israel is seeking to change rules governing the site, which allow Jews to visit but not pray.
The new flare-up came despite calls for restraint from both the United Nations and the United States, and a warning from Jordan, which has custodianship rights over Muslim holy places in Jerusalem under its 1994 peace treaty with Israel, that relations were on the line.
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