The police threw stun grenades into the crowd. An estimated 35,000 worshippers were present when the unrest began.
Police spokesman Gil Kleiman said Muslim worshippers "started rioting" at the end of Friday prayers at the shrine, a frequent flashpoint for Israeli-Palestinian violence.
One policeman was hurt in the leg before calm was restored.
Al-Aqsa mosque is the third most sacred site in Islam.
Later in the day a Palestinian on a bicycle was killed when he detonated his explosives outside a Jewish settlement in the central Gaza Strip. An Israeli army spokesman said no one else was killed or injured.
Two Israeli civilians were also killed after their car came under fire near the Green Line separating Israel from the West Bank.
"Initial details show that Palestinian gunmen opened fire on a civilian vehicle. Two people, a man and a woman, were critically injured and died soon afterwards," an Israeli military source said.
The source said the shooting took place just inside Israel, on a road close to the Green Line near the Eshkolot Jewish settlement.
In another incident, the Israeli army on Friday destroyed the houses of two fighters of the Palestinian resistance group Hamas in the southern West Bank town of Bethlehem.
Israeli controversially claimed the two - Hasan abu Sirah and Ibrahim Jundiah - were involved in a human bombing act on a Jerusalem bus in January 2002 that killed 12 people and wounded 40.
Israeli demolition of Palestinian
houses has been widely decried
The claim was contradicted by relatives of the two fighters. The family of abu Sirah said he was shot dead by Israeli troops in June 2001 after killing an Israeli intelligence officer near Bethlehem.
They said he belonged to the resistance group al-Aqsa Martyrs Brigades. His home in Bethlehem's Azza refugee camp housed five people.
The other fighter Jundiah is currently in an Israeli jail, his family said. His house, home to nine other people, was in Bethlehem's Aida refugee camp.
More than 200 houses of Palestinians have been destroyed since August 2002 in acts that have been widely criticised by human rights organisations.