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The violence began after a highly controversial tour of the mosque compound early this morning by hardline Israeli opposition leader Ariel Sharon.
Under heavy guard, Mr Sharon entered the compound with a right-wing Likud party delegation.
He crossed from the west side of the compound to the east and back again, to the sound of enraged protests from demonstrators outside.
BBC correspondent Hilary Andersson said the visit was clearly intended to underline the Jewish claim to the city of Jerusalem and its holy sites.
The site of the Al Aqsa mosque and its compound, known as Temple Mount to Jews and Haram al Sharif to Muslims, is sacred to both religions.
It lies on territory captured by Israel in the 1967 war, and is at the heart of the fierce dispute over the sovereignty of Jerusalem.
As he left the compound, Mr Sharon denied the visit was provocation, insisting he had come with a "message of peace".
"I came here to the holiest place of the Jewish people in order to see what happens here and really to help the feeling that we are now ready to move forward," he said.
But Palestinian leader Yasser Arafat described his visit as a "dangerous step".
Soon after Mr Sharon left the site, the angry demonstrations outside erupted into violence. Israeli police fired tear gas and rubber-coated metal bullets, while protesters hurled stones and other missiles.
Police said 25 of their men were hurt by missiles thrown by Palestinians, but only one was taken to hospital.
Israel Radio reported at least three Palestinians were wounded by rubber bullets.
The violence comes at a highly sensitive time for the Israeli-Palestinian peace talks.
The Israeli Prime Minister, Ehud Barak, outlined his vision for Jerusalem for the first time today in a newspaper interview.
He said he would be willing to accept two capitals - a Palestinian-controlled Al Quds next to an Israeli Jerusalem - as part of a possible peace agreement.
The peace process has been stalled over the issue of Jerusalem since the failure of the Camp David summit in July this year.
However, Mr Barak insisted he would not hand over the Temple Mount compound to Palestinian sovereignty.
Following Friday prayers the next day violence again broke out throughout Jerusalem and the West Bank.
It was the beginning of a wave of rioting which escalated into what is now known as the second Palestinian intifada (uprising), or sometimes the Al Aqsa intifada.
By the end of the first year, more than 800 people had died.
Critics say Mr Sharon knew the visit would trigger the ensuing violence and gambled on the Israeli public turning to a tough leader like him who would know how to handle it firmly.
0n 6 February 2001 he won a landslide victory, pledging to achieve "security and true peace" while insisting he would not be bound by previous negotiations with the Palestinians.
In June 2002 following a series of suicide bombings, work began on building a security wall, 640 km (440 miles) long, between Israel and the West Bank.
An effort to revive the peace process resulted in the publication of a new roadmap for peace in April 2003.
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