Updated at 11:30 a.m. ET

Jerusalem's mufti Mohammed Hussein has declared an end to recent protests, saying Muslims will again pray inside Al-Aqsa Mosque, rather than outside it, after Israeli police removed the last of the security equipment from the entrance to the holy site.

Clashes marred the return of thousands of worshippers to the site Friday afternoon.

"Shortly after returning to Temple Mount, Israeli security forces and Muslim worshippers clashed inside the compound," Ynet News reports. "Security forces used stun grenades next to the Dome of the Rock to disperse rioters, as the Red Crescent reported that 46 people were injured."

Police said one officer was hit in the head by a stone, but that the scene is now quiet.

Both the security measures and the protests had lasted two weeks after three young men, Arab citizens of Israel, killed two police officers at the religious complex, which is revered by both Muslims and Jews.

From Jerusalem, NPR's Daniel Estrin reports:

"Palestinians cheered as a truck carried away partitions and scaffolding for security cameras. Israel had set up the security equipment following a deadly shooting at the Al-Aqsa Mosque compound, also known as the Temple Mount. Palestinians accused Israel of trying to take control over the Muslim-run site and staged mass prayer protests. Israel removed the metal detectors this week, but Palestinians still protested. Police say all security equipment has now been removed."

The attack prompted authorities to install metal detectors, security cameras and other measures at the site. In response, Muslims refused to enter, with thousands of people gathering to hold prayers in the streets.

On Tuesday, the Israel Police posted an image on Twitter, showing that metal detectors had been removed from the entrance to the mosque area. Now the area is also reportedly clear of guardrails and other equipment.

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