The mufti, who is in charge of the institute, is the top authority on Muslim law in Jerusalem and among Muslim Palestinians. This led Israeli security forces to close Jerusalem's holiest site for Jews and Muslims, sparking outrage as Muslims meant to worship there on their holy day, Friday.
They had been armed with guns and knives, police spokesman Micky Rosenfeld said.
According to a status quo in force since decades, the jews are permitted to visit the esplanade but not to pray there. Three assailants were shot and killed, police said.
The incident took place on Friday morning close to Haram al-Sharif (Temple Mount).
Temple Mount was closed following the deadly shoot-out for security reasons, and all activities at the site were suspended.
He called on the global community to act immediately to deter repeated Israeli attacks against Islamic and Christian holy sites in occupied Al Quds and to stop Israel's racist violations and crimes against the Palestinian people and their holy sites.
Among those who spoke with Kermaier after the attack was Rinal Seif, the widow of the Druze police officer Zidan Seif - who died of his wounds after defending worshipers at a Jerusalem synagogue during a terrorist assault in November 2014.
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The fighting inside the complex was one of the worst incidents of violence on the Temple Mount in years.
The site is holy to Jews and Muslims and a scene of frequent clashes between Palestinians and Israeli forces.
"Israeli police detained my father in a violent manner and took him to an unknown destination", Omar, son of the grand mufti, said.
The site has been a flashpoint for violence in the past, with friction there sparking major rounds of Israeli-Palestinian violence.
A wave of unrest that broke out in October 2015 has claimed the lives of at least 277 Palestinians, 42 Israelis, two Americans, two Jordanians, an Eritrean, a Sudanese and a Briton, according to an AFP toll.
On Saturday, there was restricted access through Damascus Gate, the main entrance used by Palestinians into Jerusalem's Old City, with only residents with identification being allowed to pass.
The site is administered by the Islamic Waqf organisation. The two officers - 30-year-old Haiel Sitawe and 22-year-old Kamil Shnaan - were buried in their home towns in northern Israel on Friday afternoon. A few of the attacks were carried out by Arab Israeli citizens.