Groups of Palestinian youths threw stones and set off fireworks at Israeli police officers near one of the gates when the site was opened to visitors, police spokeswoman Luba Samri said.
The Palestinians were pushed back into al-Aqsa Mosque, Samri said, and in an attempt to control the violence, police closed access to the Temple Mount, which Muslims call Haram al-Sharif (the Noble Sanctuary).
Eyewitnesses among Muslim worshippers at the site gave a different version of events, saying hundreds of police officers raided the compound, throwing stun grenades into the mosque in an effort to clear a way to the area for Jewish protesters.
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Jordan recalled its ambassador to Israel on Wednesday in protest of "increasing Israeli escalation" at the Noble Sanctuary, Jordan's state news agency, Petra, reported.
Jordanian Prime Minister Abdullah Ensour also instructed Jordan's foreign affairs minister to submit a complaint to the United Nations Security Council about Israeli "attacks" on the Noble Sanctuary, according to Petra.
The Jewish protesters were attending a support rally for Rabbi Yehuda Glick, a right-wing activist who was shot by a Palestinian last week, ratcheting up tensions in Jerusalem and prompting the temporary closure of the Temple Mount.
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Samri said the youths had gathered in the mosque overnight, amassing rocks, fireworks and Molotov cocktails with which to attack police.
"Inside the mosque they formed obstacles to hide behind," she said. "There were violent clashes with the police."
Police went several meters into the mosque in order to clear obstacles preventing them from closing the door, Samri said, adding that Jews and tourists were now allowed back to the site.
But unrest flared again later near another gate, when police threw stun grenades and fired rubber bullets at Muslim worshippers who were chanting and praying because they weren't allowed back into the site.
Paramedics from the Red Crescent at the scene told CNN that 15 people were injured, one of them with a serious injury to the eye. Samri said police officers were injured.
The Temple Mount in Jerusalem is the holiest site in Judaism and one of the three holiest sites in Islam. With its golden dome overlooking Jerusalem, the site is said to have hosted sacred events in both the Jewish and Muslim religions.