Israel seized East Jerusalem, the West Bank and Gaza Strip in 1967. Jews could visit, but not pray there.
"It is the first time we come here without being escorted by the Waqf (the Muslim authority that administrates the site)".
The body responsible for administering the al-Aqsa mosque, al Waqf Trust, denounced the measures.
This shift has stoked Muslim fears of a purported Israeli plan to expand Jewish control there. In 2014 Jordan, the United States and Israel agreed on a number of steps to reduce tensions at the Al-Aqsa Mosque, including sticking to the status quo and restricting visits by non-Muslims.
A hospital official said one man had suffered a serious head wound from a rubber bullet fired from close range.
Netanyahu spoke to Israeli security chiefs by phone on Wednesday.
Waqf guards are posted inside the gates and have the right to turn any visitors away.
Israeli forces reopened the site on Sunday (16 July) but with heightened security, including metal detectors and turnstiles, which Jerusalem police commissioner Yoram Halevi claims are necessary to ensure worshippers' safety.
The imam had just finished leading the night prayer when Israeli police attempted to disperse worshippers by force, leaving many injured, some seriously, Palestinian Red Crescent said. "Magnetometers are vital for security. The Israeli side is trying to transform the conflict form a political one to a religious one", Abu Rudeinah said. On Sunday, Israel's Army Radio quoted the Jerusalem police chief as saying officers found dozens of knives as well as slingshots, stun grenades and binoculars, but no guns or live ammunition.
Israeli police have said that they will continue "to act to enable a return to a safe routine in the Temple Mount area, its entrances and the wider area". "We will stay outside the mosque until we get back the way it was taken from us", he said.
Jordan was reportedly not consulted about the changes by Israel.
The Shabak is anxious of an explosion by the protesters and has recommended to PM Netanyahu that the metal detectors be removed. Each summer, Hamas holds terror training camps for kids of all ages, while the P.A. encourages its youth to carry out rock and firebomb attacks, stabbings, drive-by shootings and vehicle ramming against Israelis, both security forces and civilians.
Netanyahu spoke by phone with Jordan's King Abdullah II on Saturday night, a statement from Amman said.