The grand mufti of the city, Mohammed Hussein, was detained for questioning Friday at a police station in the Old City, his son, Omar, told The Associated Press.
But despite concerns that the new measures could slow movement and spark renewed tensions, police said they appeared to be working fine and that 200 people had already passed through.
Israeli authorities said the attackers had come from the flashpoint holy site, which includes the Al Aqsa mosque and the Dome of the Rock, to wreak havoc.
Muslims have refused to enter reopened al-Aqsa Mosque protesting newly imposed Israeli security measures, including metal detectors and cameras.
Israeli forces had installed a total of nine metal detectors at the Lions' Gate (Bab al-Asbat), the Chain Gate (Bab al-Silsila), and the Council Gate (Bab al-Majlis).
He made the statements in reaction to Israel's decision to close the al-Aqsa Mosque compound to the Palestinian worshipers on Friday.
The Old City of Jerusalem on Sunday also was closed off, except to local residents and tourists, according to reports.
Israeli forces killed a suspected Palestinian militant they were seeking to arrest after he shot at them in the occupied West Bank, police and the military said.
The temple was closed for the first time in almost 50 years on a Friday, Islam's holy day. "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 attack triggered a rare phone conversation between Netanyahu and Palestinian President Mahmoud Abbas, who condemned the attack and called for the site to be reopened.
One officer was ambushed in what appears to be the Muslim Quarter of the Old City, just outside of the Al-Aqsa Mosque.
He added that "We will not receive the Al-Aqsa mosque, except as it was".
Israeli Prime Minister Benjamin Netanyahu said it was "a sad day in which our Druze brothers pay the heaviest price in our joint mission to protect the security of our country".
Security services prohibit non-Muslim prayer or engagement in other forms of worship on the Temple Mount, claiming that such activity inevitably triggers Palestinian violence. Israel views all of occupied Jerusalem as its capital, a claim that has not won global recognition.
Scuffles also broke out on Sunday, but police said hundreds of Muslims visited the site nonetheless.