His wife, an Iraqi named Umm Sayyaf, was caught and is being held in Iraq.
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.”
Umm Sayyaf, his wife, is currently in military detention in Iraq. 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.
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.
Abu Sayyaf also was known by the names Abu Muhammad al Iraqi and Abd al Ghani, they said.
More details are starting to emerge of how the raid deep in ISIS-controlled territory was carried out.
There was hand-to-hand combat during the operation, which was helicopter-borne, the sources told CNN.
About a dozen ISIS fighters were killed in the firefight at a residential building in Deir Ezzor, the sources said.
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 in the early hours of Saturday.
Preliminary information indicates that the U.S.-led coalition airdropped forces following the bombardment, it 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. While the purpose was to capture the forces had the option to kill if they deemed it necessary, the official said.
Abu Sayyaf is not a name familiar to many ISIS watchers.
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.”
CNN’s Jamie Crawford, Jim Acosta, Sunlen Serfaty, Hamdi Alkhshali, Jason Hanna and Nick Paton Walsh contributed to this report.