As in previous days, dozens of worshippers prayed outside the Haram al-Sharif compound, known to Jews as the Temple Mount, rather than enter through the metal detectors.
The attack and new security measures have increased Israeli-Palestinian tensions.
Protests and scuffles between demonstrators and Israeli police have erupted outside the site, which includes the Dome of the Rock and the Al-Aqsa mosque.
Today, a 30-year-old Palestinian carried out a car- ramming attack in the occupied West Bank near the city of Hebron, lightly wounding two Israeli soldiers before being shot dead.
A 17-year-old Palestinian who was injured yesterday during clashes in the Silwan area of east Jerusalem was in critical condition, according to official Palestinian news agency WAFA, which said he had been shot.
Palestinian hospital Makased, where the 17-year-old was being treated, alleged in a statement today that Israeli forces had entered the hospital and were disrupting operations.
Israeli police said six arrests had been made overnight in two separate areas of Jerusalem.
Police say a number of Muslims have been entering the compound, though they did not provide a number today. The compound has appeared largely empty.
On Friday, three Arab Israelis opened fire on police before fleeing to the compound, where security forces shot them dead.
Israel closed the site for two days following the attack, angering Muslims and Jordan, the site's custodian.
Israel said the closure was necessary to carry out security checks.
The site reopened on Sunday, but with metal detectors at entrances. Palestinians view the move as Israel asserting further control over the site.
It stands in east Jerusalem, seized by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.
It is considered the third holiest site in Islam and the most sacred for Jews.
Jews are allowed to visit but not pray there to avoid provoking tensions.
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