Two men were captured during the US military raid on ISIS leader Abu Bakr Al Baghdadi's hideout in northern Syria and are in American custody, the Pentagon said on Monday.
Gen Mark Milley, Chairman of the Joint Chiefs of Staff, said they were being held under tight security.
Gen Milley said Al Baghdadi's remains had been disposed of and there were no plans yet to share footage of his death.
The US said Al Baghdadi killed himself by detonating an explosive vest during the raid.
"Baghdadi's remains were transported to a secure facility to confirm his identity with forensic DNA testing, and the disposal of his remains has been done and is complete and was handled appropriately," Gen Milley said.
Alongside the general at the Pentagon on Monday, US Defence Secretary Mark Esper warned that the "security situation in Syria remains complex" after the death of the ISIS leader.
Gen Milley confirmed US President Donald Trump's claims that video and photographs existed of Al Baghdadi's final moments.
Pentagon sources told AFP on Monday that the ISIS leader was disposed of at sea by the US military.
No details were given on where or when the body was disposed of, but it was similar to the 2011 sea burial Al Qaeda leader Osama bin Laden after he was killed in a US special forces raid.
Mr Esper said that the recent reshuffling of US forces in Syria was to give Mr Trump options.
Earlier on Monday in Abu Dhabi, French Foreign Minister Jean-Yves Le Drian hailed the death of the ISIS leader.
Al Baghdadi's demise was "another blow" to the militant group after the caliphate he declared in Iraq and Syria was retaken, Mr Le Drian said.
He arrived in the UAE on Sunday as Mr Trump confirmed that the terrorist chief had blown himself up during a special forces raid on his compound in north-west Syria.
But Mr Le Drian called for re-energising the Global Coalition to Defeat ISIS to ensure the group was completely out of action.
“I salute the operation of our US ally but the fight against ISIS is not over," he said.
"We must pursue this fight collectively, within the frame of the international coalition against ISIS, while taking into consideration regional developments."
Afghanistan also welcomed the death of Al Baghdadi, calling it a significant blow to the extremist group's South Asia offshoot.
The country has long battled a Taliban insurgency but in recent years an ISIS affiliate has grown in strength, particularly in the eastern province of Nangarhar.
"The Afghan government strongly welcomes the US forces' operation that led to the death of Baghdadi," tweeted Sediq Sediqqi, a spokesman for President Ashraf Ghani.
"The death is the biggest blow to this group and to terrorism."
Saudi Arabia's Foreign Ministry said it appreciated the efforts of the US in pursuing members of ISIS.
It said the extremists "distorted the true image of Islam and Muslims around the world, and committed atrocities and crimes that contradict the most basic human values in many countries, including the kingdom".
Al Baghdadi led the terrorist group from 2010.
The ISIS affiliate in Afghanistan announced its formation in January 2015 and has since made inroads in other areas, particularly the north, sometimes bringing it into conflict with its rivals in the Taliban.
It has also attacked civilian targets in Kabul and other cities, but many Afghan officials doubt some of its claims.
Attaullah Khogyani, spokesman for the governor of Nangarhar, said the militant faction had grown weaker recently, and the death of Al Baghdadi would be a setback.
"No doubt, Al Baghdadi's death will have a deep impact on Daesh's activities in Afghanistan," Mr Khogyani said.
The US military estimates the strength of the ISIS faction to be about 2,000 fighters. Some Afghan officials put the number higher.
But Mr Khogyani said many ISIS members had been killed in clashes or had surrendered over recent months.
"Now we expect an increase in surrenders," he said.
A spokesman for the Taliban dismissed any suggestion that the Afghan ISIS branch had any link with ISIS in the Middle East.
The group was put together by the US-backed Afghan government and Nato forces, Taliban spokesman Zabihullah Mujahid said.
"The Taliban will fight them to the death," Mr Mujahid said.
Afghans have seen what lack of impact the death of a militant commander can have on a group.
The Taliban officially confirmed in July 2015 that their supreme leader, Mohammad Omar, had been dead for more than two years.
That news began a brief spell of factional rivalry but the Taliban have since grown stronger and now control more territory than at any time since their removal from power in 2001.
Eliminating Al Baghdadi gives Mr Trump a new argument for leaving Syria. But the US military campaign against extremists is far from finished.
The extremist group has ambitions to rebuild, and it remains a threat in Afghanistan, Iraq and beyond.
That means US forces, perhaps in reduced numbers, will continue hunting and attacking important ISIS targets, even as Mr Trump says he is committed to a 2016 campaign pledge to bring troops home and halt "endless wars".
US analysts say ISIS has been dealt a blow, at least symbolically. But its extremist ideology lives on.