Crowds chanted "Allahu Akbar" (God is Greatest) as a number of initial visitors entered Jerusalem's Haram al-Sharif compound, known to Jews as the Temple Mount.
The flashpoint holy site includes the Al-Aqsa mosque and the Dome of the Rock.
But midday Muslim prayers were held outside the site due to the new security measures.
"We reject the changes imposed by the Israeli government," Sheikh Omar Kiswani, Al-Aqsa director, told reporters outside.
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Three Arab Israeli assailants opened fire on Israeli police Friday in Jerusalem's Old City before fleeing to the compound.
Israeli authorities said they had come from the flashpoint holy site to commit the attack.
Israel took the highly unusual decision to close the Al- Aqsa mosque compound for Friday prayers, triggering anger from Muslims and Jordan, the holy site's custodian.
The site remained closed on Saturday, while parts of Jerusalem's Old City were also under lockdown.
Israeli authorities said the closure was necessary to carry out security checks and announced it would reopen the compound today.