Earlier in the day, Israeli forces attacked Palestinians staging a sit-in outside the compound's main entrance for the third consecutive day after Tel Aviv implemented the new measures that ban worshipers from performing their prayers freely in the mosque.
Tensions have soared since Friday.
According to Palestinian eyewitnesses, Israeli soldiers responded with a barrage of bullets, killing the driver.
The Waqf also said in a statement on Wednesday that "the longer Israel delays the removal of the metal detectors, the worse it is going to get" as more Palestinian worshippers converge outside of Damascus and Lion's Gates in occupied East Jerusalem for prayers.
In an interview with Asharq Al-Awsat, Sheikh Hussein called on all Palestinians to boycott those procedures and preferred that Muslims pray in the streets and corridors of Jerusalem rather than to enter Al-Aqsa in a humiliating way.
"We call for an end to all the Zionist measures and for the extremist government to take its hands off the blessed Al Aqsa mosque", it said.
The incident took place before dawn in the West Bank village of Nabi Saleh, near the city of Ramallah, and no Israeli casualties were reported.
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Saudi Arabia's King Salman spoke with senior United States officials seeking to pressure Israel to reopen of the Al Aqsa Mosque in Jerusalem, according to Arabic news site Elaph.
Leaders of the Muslim religious trust that runs the site urged worshippers not to pass through the metal detectors, describing them as a violation of a delicate status quo with Israel and held a prayer service next to the devices.
Conflicts over the walled holy site, revered by Muslims and Jews, have repeatedly triggered Israeli-Palestinian confrontations.
The compound houses the al-Aqsa Mosque and the Dome of the Rock shrine, Islam's third holiest site after Mecca and Medina.
The vote came amidst spiraling tensions around the al-Aqsa mosque compound in East Jerusalem, with daily clashes between Muslim worshippers and the police.
"We will not enter through these metal detectors", he added. "I decided that as of tomorrow, in the framework of our policy of maintaining the status-quo, we will gradually open the Temple Mount, but with increased security measures". The Muslim religious authority charged with managing Temple Mount has also expressed its anger over metal detectors being installed at the site.
"It is no longer acceptable to leave the situation as it stands", Abbas's spokesman, Nabil Abu Rudeinah, said in an interview on Palestine TV. Jordan's stance is that anything installed at the site must be approved by the Waqf, or Muslim administration, and can not change the status quo, said the official.