A police force that entered the holy site stopped the rioters and dispersed the crowd. Two policemen were lightly injured and one woman was arrested for disruption of public order.
The Temple Mount was consequently closed for visitors.
Police spokesman Micky Rosenfeld said the violence erupted when police opened one of the walled compound's gates to non-Muslim visitors, according to the regular visiting hours.
"Stones and a number of Molotov cocktails were thrown at police," he told AFP.
"Police responded by using stun grenades and entered the Temple Mount area," he added, using the Jewish term for the site where tradition says the biblical Jewish temples once stood.
A later police statement said that a woman was arrested and two policemen were slightly injured.
The temple site is revered as Judaism's holiest place. The compound also houses the Dome of the Rock and the Al-Aqsa mosque, and is considered the third holiest site in Islam.
Although non-Muslim visitors are permitted, Jews are not allowed to pray at the site.
Rosenfeld could not say if Jews were among those seeking to visit the site on Sunday.
AFP contributed to this report