Police spokeswoman Luba Samri told AFP that Palestinian youths had thrown stones and petrol bombs at police, injuring several, who had "pushed the rioters inside the Al-Aqsa mosque."
The loud report of sound grenades echoed through the Old City as police closed off access to the sprawling plaza, which lies in the heart of the Old City, to prevent the unrest from spreading.
The clashes were apparently triggered by the early morning visit to the site by a group of Jewish visitors ahead of the start of the two-day Rosh Hashana holiday, which begins at sundown.
Two of them were arrested for violating an order barring Jews from praying at the site, she said.
More From This Section
Near the compound, police were seen throwing sound bombs at a small crowd of Palestinians waiting just outside Lion's Gate, one of the entrances to the Old City.
One policeman suffered head injuries in the scuffle. A total of five policemen were injured during the clashes, one of whom was in moderately serious condition, Samri said.
The Al-Aqsa compound is the scene of frequent clashes between Palestinians and Israeli police.
Security forces regularly impose an age limit on worshippers attending Muslim weekly prayers on Fridays, keeping out men under the age of 50.
Non-Muslim visits to the Al-Aqsa complex are permitted and regulated by police, but Jews are not allowed to pray at the site for fear it could trigger major disturbances and unrest.
The Old City and wider Israeli-annexed Arab east Jerusalem have been the scene of regular, violent clashes since the murder of a Palestinian teenager by Jewish extremists in July.
On September 7, 16-year-old Mohammed Sinokrot died from injuries sustained when he was shot by Israeli border police in east Jerusalem, bringing thousands of angry demonstrators on to the streets.