The ISIS commander, identified by his nom de guerre Abu Sayyaf, was killed in a heavy firefight after he resisted capture in the raid at al-Omar, U.S. Defense Secretary Ash Carter said in a statement.
The officials identified Sayyaf's captured wife as Umm Sayyaf, an Iraqi. She is now being held in Iraq.
The U.S. government did not release Sayyaf's real name.
The ground operation was led by the Army's Delta Force, sources familiar with the mission told CNN. There were about two dozen members of Delta Force involved, sources said.
Delta Force entered the target area on Blackhawk helicopters and V-22 aircraft, a U.S. official familiar with the operation said. ISIS fighters defended the multistory building from inside and outside positions.
Abu Sayyaf was killed as he "tried to engage" U.S. troops, the official said.
Carter said he had ordered the raid at the direction of President Barack Obama. All the U.S. troops involved returned safely.
National Security Council spokeswoman Bernadette Meehan said Obama had authorized the raid "upon the unanimous recommendation of his national security team" and as soon as the United States was confident all the pieces were in place for the operation to succeed.
"Abu Sayyaf was a senior ISIL leader who, among other things, had a senior role in overseeing ISIL's illicit oil and gas operations -- a key source of revenue that enables the terrorist organization to carry out their brutal tactics and oppress thousands of innocent civilians," she said in a statement. "He was also involved with the group's military operations."
Abu Sayyaf was a Tunisian citizen, a senior administration official said.
A U.S. official with direct knowledge of the intelligence and the ground operation said Sayyaf had expertise in oil and gas and had taken an increased role in ISIS operations, planning and communications.
"We now have reams of data on how ISIS operates, communicates and earns its money," the official told CNN, referring to some of the communications elements, such as computers, seized in the raid.
A young woman from the Yazidi religious minority was rescued.
"We suspect that Umm Sayyaf is a member of ISIL, played an important role in ISIL's terrorist activities, and may have been complicit in the enslavement of the young woman rescued last night," said Meehan. ISIL is an alternative acronym for ISIS.
Meehan said Umm Sayyaf was being debriefed about ISIS operations, including any information she may have on hostages held by the terror group.
Abu Sayyaf and his wife were suspected to be involved in or have deep knowledge of ISIS hostage operations, a U.S. official with knowledge of the operation told CNN. A team from the FBI-led High Value Interrogation Group is expected to interrogate the wife, the source said. They will seek to figure out what she may know about the capture, movement and treatment of hostages.
But Michael Weiss, author of "ISIS: Inside the Army of Terror," said Abu Sayyaf was largely unknown to close observers of the organization.
Weiss said he's skeptical the United States would risk lives to capture the head of ISIS's oil operations. ISIS hasn't made significant money from captured oil fields since U.S. bombers began striking its infrastructure, he said.
A Pentagon spokesman confirmed in February that oil is no longer a main source of revenue for ISIS.
But risking American lives to capture Abu Sayyaf makes sense to Derek Harvey, a former U.S. Army colonel, intelligence officer and the director of the Global Initiative for Civil Society and Conflict at the University of South Florida.
"The most important thing about the raid is not getting Abu Sayyaf; it's getting his records," Harvey said.
Harvey asserted that Sayyaf was one of ISIS's top financiers, with likely access to the group's contacts with banks, donors, Turkish and Lebanese business interests as well as links to criminal and smuggling networks.
Harvey said Sayyaf had undeniable value as a target because ISIS is also a business.
"They're meticulous record-keepers," he said.
Meehan's statement added that Obama is "grateful to the brave U.S. personnel who carried out this complex mission as well as the Iraqi authorities for their support of the operation and for the use of their facilities, which contributed to its success."
Meehan said the U.S. did not coordinate with nor advise Syria in advance of the operation.
"We have warned the Assad regime not to interfere with our ongoing efforts against ISIL inside of Syria," she said, adding that the "brutal actions of the regime have aided and abetted the rise of ISIL and other extremists in Syria."
There is reason to believe that Abu Sayyaf may have been in contact with ISIS leader Abu Bakr al-Baghdadi, sources familiar with the operation told CNN.
Although he was not taken alive, U.S. forces did capture some of his communications equipment, the sources said.
More details are starting to emerge of how the overnight raid deep in ISIS-controlled territory was carried out.
Delta Force was part of a multi-branch force of about 100, the sources told CNN. There was hand-to-hand combat during the operation, which was helicopter-borne, the sources told CNN.
The U.S. forces blew a hole in the side of the building, entered through the hole and encountered more ISIS fighters, the source said.
ISIS combatants tried to use human shields, but U.S. troops managed to kill the fighters without hurting the women and children, the official said without elaborating.
One of the Blackhawk helicopters took a couple of rounds of fire but was airworthy and took off, the source said.
The U.S. forces had an Arabic interpreter with them. They came across ancient artifacts in the building, including coins, which they are examining now, the source said.
About a dozen ISIS
fighters were killed in the firefight at a residential building in Deir Ezzor, the sources said. A senior administration official told CNN the purpose of the mission was to capture the target, but he engaged U.S. forces so was killed.
Meanwhile, the Syrian Observatory for Human Rights, a London-based monitoring group, said at least 19 ISIS militants had been killed by coalition bombing targeting ISIS' location in al-Omar oil field in eastern Deir Ezzor.
Preliminary information indicates that the U.S.-led coalition airdropped forces following the bombardment, it said.
There are six oil and gas fields in Deir Ezzor, all of which fell into ISIS hands in July last year. They include al-Omar oil field, Syria's largest oil facility.
Abu Sayyaf is not a name familiar to many ISIS
watchers and may well be a pseudonym. Sources familiar with the operation said he also was known by the names Abu Muhammad al Iraqi and Abd al Ghani.
But the fact that the United States clearly had him under close watch and was ready to put its forces at risk to carry out a ground raid, rather than ordering a drone strike, suggests the target was seen as very valuable.
CNN National Security Analyst Peter Bergen said the decision to send in U.S. Special Operations forces into Syria was unusual, but not unprecedented.
"Taking out the guy who runs effectively the most important financing stream is obviously significant, but what's really significant is the computer records and all the materials that he would have with him as the head of this financing arm, if indeed that is the case that he is really that important," said Bergen.
The potential to seize valuable intelligence material and documents may have been what led the U.S. government to opt for a high-risk ground operation rather than a bombing mission, he said.
Such targeted operations push ISIS to be more careful about how they organize themselves and run their operations, he said. "They are going to be looking over their shoulder."
Interrogation of Umm Sayyaf may also yield valuable information.
For weeks, unconfirmed reports have been circulating that al Baghdadi was seriously injured in an airstrike back in March in northern Iraq. That has led to speculation over who might emerge as his successor if he is incapacitated.
Iraqi authorities have said Abu Alaa al-Afari, his top deputy, and a senior ISIS security figure named Akram Qirbash were recently killed in an airstrike.
ISIS advance in Ramadi
The U.S. operation comes at the same time as a monthslong fight for the key central Iraqi city of Ramadi appears to be going ISIS' way.
The Islamist extremist group captured the police headquarters, the Ramadi Great Mosque and even raised its trademark black flag over the provincial government building, sources said Friday.
The ISIS push began Thursday, with armored bulldozers and at least 10 suicide bombings used to burst through gates and blast through walls in Ramadi, according to a security source who has since left the city. Dozens of militants followed them into the city center.
Iraqi and allied forces have fought back, with a number of coalition airstrikes targeting ISIS assets around Ramadi, in Anbar province.
On Saturday, ISIS fighters pulled out of key parts of Ramadi, including the main buildings in the middle of the city, according to two Iraqi security sources in the city who did not want to be named because they're not authorized to speak to the media.
ISIS controls a huge swath of territory across Iraq and Syria, where it is chief among the opposition groups fighting to unseat long embattled Syrian President Bashar al-Assad.