After the morning prayers, announcers called on the Muslim worshipers to remain at the site and block all entrances to the area for the Jews.
Dozens of Palestinians were injured including Grand Mufti of Al-Quds, Sheikh Muhammad Hussein and former minister Adnan Al-Hasani, Palestinian media reported.
Israeli security forces and Palestinian worshippers clashed at the al-Aqsa compound on Sunday as overlapping Jewish and Muslim holidays led to tensions there, which resulted in the wounding of 61 Palestinians.
During the night, thousands of Jewish worshipers visited the Western Wall, the closest spot to the Temple Mount where Jews can pray, to read Lamentations and other traditional Tisha B'av liturgy.
Scuffles ensued and the crowd fled as the sound grenades exploded and smoke wafted through the compound, witnesses said.
"It's our mosque, it's our Eid", said Assisa Abu Sneineh, 32, adding she was there when the clashes erupted.
In recent years, ultra-nationalist Israeli Jews have been challenging the status quo, demanding the government increase the numbers of Jewish visitors to the site and allow prayers.
Israeli police officers run during clashes with Palestinians by the Dome of the Rock Mosque in the Temple Mount compound in Jerusalem, Sunday, June 2, 2019.
"A number of Palestinians were injured during clashes with Israeli forces inside the Al-Aqsa mosque compound", said Firas al-Dibs, a spokesman for Jerusalem's Jordan-run Religious Endowments Authority.
Senior Palestinian official Hanan Ashrawi called Israel's response "an act of recklessness and aggression".
After the confrontations died down, Jerusalem District Police Chief Doron Yedid said on Kan radio that he had lifted the visiting ban and Jewish visitors had then entered the area under heavy police guard.
He said that Israel has no sovereignty over the Al-Aqsa mosque and that Israel is occupying the mosque.
In a move never recognised by the worldwide community, Israel annexed the entire city in 1980, claiming it as the self-proclaimed Jewish state's "eternal and undivided" capital.
Eid al-Adha commemorates God's testing of Abraham's faith by commanding him to sacrifice his son.