Najaf, Iraq ? Militants filed out of the Imam Ali Shrine, closed the doors behind them and turned over the keys to Iraq’s top Shiite cleric Friday, symbolizing their acceptance of a peace deal to end three weeks of devastating fighting in this holy city.

By Friday afternoon, dozens of Iraqi police and national guardsmen surrounded the shrine compound — many kissing its doors and weeping — as the government began to re-establish control over the Old City of Najaf. Some residents of the devastated neighborhood waved to them and yelled out, “Welcome. Welcome.”

U.S. forces still maintained their positions around the holy site, with tanks about 300 yards from the shrine and jet fighters flying overhead, but the fierce clashes of previous days had ended and most of the battered city had fallen calm.

“Today, the Najafis can sleep well,” Hamed al-Khafaf, an aide to Grand Ayatollah Ali al-Sistani, told Al-Arabiya television.

Dozens of the militants loyal to Muqtada al-Sadr piled their Kalashnikov rifles in front of the firebrand cleric’s office here, but thousands of others were believed to be still armed, and some were seen pushing carts full of machine-guns and rocket launchers through a narrow alley.

The peace plan, presented by al-Sistani on Thursday and accepted by the government and al-Sadr, calls for the cities of Najaf and Kufa to be declared weapons-free, for all foreign forces to withdraw from Najaf and leave police in charge of security and for the government to compensate those harmed by the fighting.

The plan allowed al-Sistani, the most revered Shiite cleric in Iraq, to exercise his considerable authority and prove that he could succeed where other peace emissaries had failed. It gave the interim government control of the city, disentangled U.S. forces from the persistent violence here and let al-Sadr and his militants walk away free.

But it also allowed al-Sadr to keep his militia, which fought with U.S. forces here in the spring and could take up arms again.

A U.S. defense official, speaking on the condition of anonymity, said the U.S. military was wary of any agreements in Najaf because al-Sadr’s militia had used previous breaks in fighting to regroup and rearm.

Civilians welcome Iraqi police making their way through the streets of the southern Iraqi city of Najaf. Guns were largely silent in Najaf on Friday for the first time in weeks, after Iraq's top Shiite cleric made a dramatic return to this holy city and swiftly won agreement from a rebel cleric and the government to end three weeks of fighting between his militia and U.S.-Iraqi forces.

But the White House welcomed the agreement, though it cautioned that the administration was not aware of all the details.

“We welcome these steps to resolve the situation surrounding the shrine of Ali without further violence and we support the efforts of the Iraqi government to make sure that the rule of law applies throughout the country,” White House spokesman Scott McClellan said.

The crisis appeared resolved Friday morning when al-Sadr issued a statement broadcast over the shrine’s loudspeakers ordering his Mahdi Army militia fighters to lay down their arms and leave Najaf and Kufa.

“To all my brothers in the Mahdi Army … you should leave Kufa and Najaf without your weapons, along with the peaceful masses,” his statement said.

The doors of the shrine were shut and the keys were handed over to al-Sistani’s office, a symbolic and crucial step in ending the crisis.