The United States carried out limited air strikes in the area during the operation, the first time it has expanded its more than three-week air campaign against IS beyond north Iraq.
Iraqi forces kept up the momentum on Monday, with Kurdish peshmerga fighters and Shiite militiamen retaking Sulaiman Bek, a town north of Amerli that had been an important militant stronghold.
"Within a few hours, we were able to clear the town completely," the commander of the Shiite Badr militia, Transport Minister Hadi al-Ameri, told AFP in Sulaiman Bek.
Fighters celebrated in the abandoned town, firing in the air, chanting anti-IS slogans and showing off a captured black flag of the group.
Security forces and Shiite militiamen later retook the nearby town of Yankaja from the militants, officials said.
- 'Graveyard' for jihadists -
Before the operation, the mainly Shiite Turkmen residents of Amerli were endangered both because of their faith, which jihadists consider heresy, and their resistance to the militants who had besieged the town for 11 weeks.
UN Iraq envoy Nickolay Mladenov had warned that they faced a "massacre".
Maliki visited Amerli on Monday, vowing that "Iraq will be a graveyard" for IS.
A convoy of militia fighters arrived in the town to a rapturous welcome of ululations and celebratory gunfire.
But scuffles also broke out among hungry residents when the fighters began to distribute food and water.
The operation to break the siege of Amerli was launched on Saturday.
The government's reliance on Shiite militiamen in this and other operations risks entrenching groups which themselves have a history of brutal sectarian killings.
The United States said it had launched four air strikes in the Amerli area.
In doing so, it effectively supported operations involving militia forces which previously fought against US troops in Iraq.
David Petraeus, a former commander-in-chief of US-led forces in Iraq, has warned against America becoming an "air force for Shiite militias".
Meanwhile, more pledges were made to provide arms to Iraq's Kurds, who are battling jihadists in the north and east.
Backed by US air strikes, Kurdish troops have succeeded in clawing back some areas that fell to the jihadists last month.
The air campaign continued on Monday, with American warplanes carrying out strikes against IS targets in the area of Mosul dam in northern Iraq.
Germany has announced that it will send anti-tank rocket launchers, rifles and hand grenades to support Kurdish forces.
On Monday, Chancellor Angela Merkel made an impassioned 25-minute speech in support of arming the Kurds, saying: "We have the opportunity to save lives and stop the further spread of mass murder in Iraq."
- At least 1,420 killed -
She also said an estimated 400 German nationals had travelled to Iraq and Syria to fight alongside jihadists, and that "we must fear these fighters could return one day".
Various Western countries have expressed such fears, and British Prime Minister David Cameron on Monday announced tougher measures against suspected returning jihadists.
These would include banning suspects who are British from returning to the UK, and enhanced police powers to temporarily strip departing suspects of passports.
The United Nations mission to Iraq said on Monday that at least 1,420 people were killed in Iraq violence in August and 1,370 were wounded.
It said these figures did not include Anbar province, west of Baghdad, acknowledging difficulties in verifying information from areas outside government control.
More violence struck Baghdad on Monday, when two car bombings killed at least nine people, officials said.
IS and its allies control a large swathe of northeastern Syria as well as territory in Iraq, and its rule has been marked by atrocities.
"The reports we have received reveal acts of inhumanity on an unimaginable scale," deputy UN rights chief Flavia Pansieri said Monday.
The 47-member UN Human Rights Council in Geneva unanimously agreed to send an emergency mission to Iraq to investigate IS atrocities.
"We are facing a terrorist monster," Iraqi Human Rights Minister Mohammed Shia al-Sudani told the council, decrying acts "equivalent to genocide and crimes against humanity".
Washington has said operations in Syria will be needed to defeat IS, but has so far ruled out any cooperation with the Damascus regime against the jihadists.