Men aged below 40 were stopped from entering al-Aqsa mosque
At least three Palestinians were killed by Israeli tank fire in the Rafah sector of southern Gaza Strip, Palestinian hospital sources said.
The violence is further undermining an official ceasefire signed between the two sides, which Washington sees as an important part of its global campaign against terrorism.
But in a separate development on Friday, Israeli and Palestinian security officials agreed measures to ease the conflict in the Palestinian territories.
The Israeli Defence Ministry said Israel had promised to open the Rafah border crossing between the Gaza Strip and Egypt on Sunday.
Israeli officials, who met a Palestinian delegation at US-sponsored talks in Tel Aviv, also promised to restore free traffic movement in major Palestinian towns if the situation on the ground calmed down.
The Palestinians for their part agreed to "solidify the ceasefire" and to meet again next week.
Despite the truce, a Palestinian man and a 10-year-old Palestinian boy were shot dead in clashes with Israeli soldiers in the West Bank town of Hebron. A Palestinian youth was shot dead during rioting in Bethlehem.
Also in Hebron, two Israelis were slightly wounded in Hebron after Palestinian gunmen fired on their car. A Palestinian was critically injured near Rafah.
Late on Friday, three Palestinians died and three were injured, two seriously, when an Israeli tank fired a shell at a group of people near the al-Nur mosque in Rafah, Palestinian security officials said.
The officials were quoted by Associated Press saying they were looking into the possibility that the group were laying an explosive to be detonated against Israeli troops.
Silent protest
During the day, Palestinians observed three minutes of silence throughout the West Bank and Gaza Strip, in a show of anger at Israeli policies.
Israeli police took extra security measures, sharply restricting access to the al-Aqsa mosque compound in Arab East Jerusalem.
About 1,000 additional police were deployed across the city, around the old city entrances and around the mosque itself.
The BBC's Kylie Morris in Gaza says the mood has been tense since five Palestinians were killed by Israeli troops in the Gaza Strip on Thursday.
There were also demonstrations in other parts of the Arab world, with more than 1,000 people shouting slogans supporting the intifada after Friday prayers at Cairo's al-Azhar, the most respected institution of Sunni Islam.
In Jordan, protesters urged Arab states not to take part in the coming US offensive against terrorists in Afghanistan, while thousands attended anti-Israel protests in Palestinian refugee camps in Lebanon.
Protesters marched through the Syrian capital, Damascus, in silence out of respect for Palestinians who have died in the conflict,
Controversial visit
Black and white posters in Gaza City declare that the intifada should continue until Israeli occupation ends.
The uprising broke out on 28 September last year when Palestinians frustrated with the direction of the peace process rioted after the then Israeli opposition leader, now prime minister, Ariel Sharon visited the compound.
The al-Aqsa mosque is the third holiest site in Islam, while to the Jewish people, who call it the Temple Mount, it is the holiest. The remains of the first and second Jewish temples are believed to lie beneath the site.
More than 600 Palestinians and 160 Israelis have died in the last 12 months of violence.
A UN report estimated that the conflict had cost the Palestinian economy around $2bn.
And the intifada has caused a shift in Palestinian politics, with surveys showing an increase in popularity of Islamist militant groups like Hamas and Islamic Jihad
On Thursday, a 15-year-old boy was shot dead by Israeli soldiers who then killed a Palestinian man wandering near a Jewish settlement. Palestinian officials said the man, who was mentally disturbed, was riddled with bullets.