A 25-year-old protester has succumbed to his wounds, becoming the fifth Palestinian to be killed by Israeli forces and settlers in two weeks of violence as tension mounts over discriminatory restrictions at al-Aqsa Mosque.

Muhammad Kanan, who had been shot in the head three days earlier, died late on Thursday in a hospital in the central occupied West Bank city of Ramallah, the Palestinian Ministry of Health said.

Kanan had joined thousands of Palestinians in the streets to rally against extra restrictions at Jerusalem's al-Aqsa Mosque compound, protesting in Hizma, his hometown near Jerusalem.

Israeli soldiers and police cracked down on extended protests on Friday.

Police announced for the second week running a ban on men under the age on 50 attending the holy site, and closed several gates to the compound.

That announcement came hours ahead of Friday prayers, when thousands of Muslims typically worship in congregation at al-Aqsa Mosque.

Police fired water cannon and tear gas at protesters in Bethlehem, and there was a high police presence close to al-Aqsa compound.

"We were barred from entering al-Aqsa," Salim abu Hani told Al Jazeera. "We came from Beersheba to pray. We will pray in the street; there is no other way."

Beersheba is more than 100 kilometres from Jerusalem.

"The situation has gotten worse," said 34-year-old Abdullah abu Hani, also from Beersheba. "God willing it will become better and [the Israeli authorities] will remove the checkpoints."

Samira Edrees, a resident of the Old City, said she refused to pray inside the compound "because nothing has been achieved".

"How can I pray in there when there is no peace? How can I go in when my brother and son are barred? The police are acting like a gang," she told Al Jazeera.

Dozens of worshippers were subject to identification checks by Israeli police.

Al Jazeera's Imran Khan, reporting from Jerusalem's Damascus Gate, said police were deployed in large numbers.

"There's a real atmosphere of tension," he said, explaining that Israeli forces were restricting movement from checkpoints between occupied East Jerusalem and the rest of the West Bank.

Israel installed metal detectors and turnstiles at the mosque, the third holiest site for Muslims, after an alleged attack on July 14 when three Palestinian citizens of Israel fatally shot two Israeli policemen, and were later killed themselves.

Palestinians viewed the restrictive measures - which have since been removed - as an encroachment of Israeli control over the holy site, and a form of collective punishment.

They feared that Israel was attempting to change the status quo of al-Aqsa, which gives Muslims religious control over the compound and Jews the right to visit, but not pray there, and launched a boycott.

Instead of praying at the mosque, they worshipped in the streets and demonstrated against the measures.

Men under 50 banned again

Palestinian religious leaders who were satisfied with the eased restrictions declared an end to the boycott, and thousands of Palestinian worshippers returned to the mosque on Thursday for the first time since July 14.

But renewed clashes followed, with Israeli forces firing stun grenades, tear gas and sound bombs in the mosque's compound, wounding more than 100 people.

Jamal Zahalka, a Palestinian politician in Israel's Knesset, said Palestinians would "continue to defend al-Aqsa and Jerusalem and insist an end to the occupation".

"If there is no occupation, there is no struggle against occupation," he told Al Jazeera.

The compound, known to Muslims as the Noble Sanctuary and to Jews as the Temple Mount, is in occupied East Jerusalem.

Over 12 days of protests, Israeli forces wounded more than 1,000 Palestinians during clashes, according to the Palestinian Red Crescent.

Three Palestinians were killed last Friday during "Day of Rage" protests across the West Bank, including East Jerusalem.

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Later that night, a Palestinian assailant hopped the fence of Halamish, a Jewish-only settlement in the West Bank, and killed three Israelis in their home.

Raed Saleh, a resident of East Jerusalem, said that re-entering the compound on their own terms was a victory for Palestinians.

"We never saw this kind of win for our people," he told Al Jazeera. "People are coming from everywhere just to support us in this occasion.

"The Israeli government will now understand that Palestinians from Jerusalem will not accept everything they [Israelis] will tell them. We control ourselves. No one is controlling us."

Al Jazeera's Stefanie Dekker, reporting from East Jerusalem, said Palestinians view the removal of the cameras and metal detectors as "a victory for the people".

"Everyone we speak to says this is a historic moment," she said.

Yoram Halevy, the Israeli police chief in Jerusalem, threatened Palestinians and urged them not to continue their protests on Friday.

"If they try to disrupt the order [on Friday], there will be casualties," he said, according to Israeli media reports. "Do not try us. We know how to react vigorously."

Additional reporting by Ibrahim Husseini in Jerusalem.