Fighting in the holy city was concentrated around the 1920 Revolution Square in the early hours of Tuesday, less than two kilometres from the town centre.
Occupation forces continue to engage Mahdi Army militiamen loyal to cleric Muqtada al-Sadr who vehemently rejects US authority.
Both sides denied responsibility for raking Ayat Allah Ali al-Sistani's residence with bullets.
The golden dome of Imam Ali's mosque, the most revered and historic Shia sanctuary, has also had four holes blown through it.
US forces said on Monday they killed 50 of al-Sadr's supporters in heavy overnight clashes in the city and in al-Nasiriya, further south.
US Brigadier-General Mark Kimmitt confirmed his forces estimated they had killed 30 Iraqis in Najaf alone, 17 of them "in the vicinity of the shrine area".
But locals described seeing supporters dragging their dead away, indicating some may not have been accounted for.
Al-Nasiriya air raids
In al-Nasiriya, Kimmitt said occupation forces killed 20 al-Sadr loyalists in air strikes in the Italian-patrolled city on Monday morning.
"Coalition fixed-wing aircraft engaged five targets this morning. The targets were five vehicles that had been observed unloading and loading ordnance," Kimmitt told a Baghdad news conference.
Mahdi Army militiamen refuse to
leave Imam Ali's shrine
"We estimate that 20 enemy persons were killed during these strikes," he said.
For more than a month, al-Sadr's militia have been fighting in the holy cities of Najaf, Kufa and Karbala, as well as al-Nasiriya, Basra and Amara further south, in a major resistance movement that has threatened to spark a wider uprising by Iraq's Shia community.
US troops have been stepping up the pressure on the fighters in the past two weeks, pressing closer to sacred shrines despite warnings from Iran's leadership to stay out of the holy cities.