It is the third-holiest site in Islam and the most sacred for Jews as the site of the first and second ancient temples. Several young men clambered onto the mosque's roof to affix Palestinian flags, which Israeli police soon confiscated.
Following a tense period marked by multiple deadly terrorist attacks and widespread rioting by Palestinians, Israeli Prime Minister Benjamin Netanyahu offered an explanation of sorts for his decision to remove added security from the Temple Mount compound.
Arab Foreign Ministers held an urgent meeting in Cairo to probe the recent Israeli violations and procedures in East Jerusalem. Israel repatriated the guard to a hero's welcome, saying he had fired in self-defense against an attack that may have been spurred by pro-Palestinian sentiment. Three Israelis were stabbed to death in a West Bank settlement by a Palestinian attacker the same day.
Earlier on Thursday, Muslim elders declared themselves satisfied that Israeli authorities had removed all the new security measures - mainly metal detectors and CCTV cameras - and reverted to the set-up before July 14.
"We praise this stand in the past two weeks outside Al Aqsa and we want this stand to continue outside Al Aqsa and now inside Al Aqsa", he said, urging worshippers to return to pray.
Jordan, the custodian of Jerusalem's Muslim holy sites, welcomed the removal of the security measures but said Israel should not provoke Palestinians there.
Palestinian political factions issued statements supporting the Waqf, which looked likely to help defuse the unrest. Netanyahu said the extra security was needed to ensure safety at the site, which is popular with tourists.
Roads around Jerusalem's Old City, where the compound is located, were closed and some 3,500 police were deployed. Jews pray under heavy security at the Western Wall at the foot of the elevated plaza. It annexed the area and declared it part of its "indivisible capital".
The holy compound lies in east Jerusalem, seized by Israel in the Six-Day War of 1967 and later annexed in a move never recognised by the global community.
Palestinians viewed the move as Israel asserting further control over the site.
Netanyahu's comments this Sunday focused on what he referred to as the "wider" picture with regard to security for the Jewish state, alluding to additional considerations of which, he claims, the public is unaware.
The measures as well as the killings and repression by Israel violate the most basic human rights, according to the statement.
"Instead of bolstering our sovereignty in Jerusalem, a message was relayed that our sovereignty can be shaken".