Clashes broke out between Palestinian protesters and Israeli police following Friday prayers at the Al-Aqsa Mosque compound.
Police fired stun grenades and tear gas, and Palestinians hurled rocks after hundreds took part in a celebratory demonstration in which they waved Palestinian and Hamas flags and cheered the militant group.
There are conflicting reports about what sparked the violence at the holy site, which is revered by both Muslims and Jews.
The official Palestinian news agency Wafacites witnesses as saying that after Friday prayers worshippers stayed at the site to celebrate the ceasefire ending the 11-day conflict between Palestinian militants in Gaza and Israel. Israeli police, it adds, subsequently “raided the courtyards and started firing rubber-coated rounds and tear-gas at the worshippers”.
At least 15 people were hit by rubber-coated rounds, while many others were affected by tear gas or were beaten by officers, according to Wafa.
Clashes between protesters and police there earlier this month were one of the main triggers for the war.
Earlier thousands took to the streets of Gaza as a cease-fire took hold at 2 a.m.
Young men waved Palestinian and Hamas flags, passed out sweets, honked horns and set off fireworks.
Celebrations also broke out overnight in east Jerusalem and across the occupied West Bank.
Israel captured all three territories in the 1967 war and the Palestinians want them for their future state.
The International Committee of the Red Cross has confirmed that the Kerem Shalom crossing to Gaza has been re-opened.
Local media reports had previously conflicted about whether the major corridor into Gaza was letting traffic through. But the ICRC said it had used the crossing – located on the borders of Israel, Gaza and Egypt – to ferry medical supplies and equipment to Palestinians in the territory.