The Qatar-based cleric flew to Egypt from Doha on Monday to deliver a speech at the Egyptian Journalists' Syndicate in Cairo, where he condemned the Arab governments' silence towards the "violation of Al Aqsa's holiness" by Israeli settlers and occupation forces.
Tensions erupted in the area known as Al Haram Al Sharif to Muslims and the Temple Mount to Jews last week when a group of non-Muslims entered the compound, which is the third holiest venue in Islam and the most important in Judaism.
While Israeli authorities said that the group was composed of French tourists, Palestinians believed that they were Israeli extremists entering the mosque in celebration of the Jewish Sukkot festival.
Further confrontations took place Sunday as tens of Palestinians entered the mosque overnight amid rumors that larger numbers of Israelis will be allowed to enter the mosque, before Israeli forces shut down the holy site.
Muslims under 50 years old were later banned from praying inside the mosque and on Monday, thousands of Jewish worshipers prayed at the Western wall below Al Aqsa for religious celebrations.
Qaradawi, who is well-known for his controversial fatwas, urged all Egyptian clerics to dedicate Friday prayer speeches to showing solidarity with Al Aqsa and asking Muslims to gather for peaceful protests afterward.