The soldiers used stun grenades to disperse the Palestinians, police spokesperson Micky Rosenfeld told AFP, adding that there was "high tension" ahead of discussions expected in the Israeli parliament later Tuesday of a plan to annex the holy site, known to Jews as the Temple Mount.
He added two policemen were injured and three protesters were arrested.
The Israeli Knesset, or parliament, is due to debate in the evening a bill introduced by MP Moshe Feiglin, a hardline member of Prime Minister Benjamin Netanyahu's Likud party, which envisages the "application of Israeli sovereignty" over the compound.
No vote is envisaged at the end of debate. Netanyahu is opposed to the bill and commentators say it is unlikely to attract much support.
The Al-Aqsa compound, which lies in al-Quds' Old City, is a flashpoint because of its significance to both Muslims and Jews.
Sitting above the Western Wall plaza, it houses the Dome of the Rock and Al-Aqsa mosques and is Islam's third-holiest site.
The site is in Israeli-annexed east al-Quds but administered by Muslim religious authorities.
BA/BA